Running a molecular dynamics simulation of the Dickerson (DNA) dodecamer

• Create a clean directory and cd in it.

• Get the CHARMM force field parameter and topology files :

• cp /usr/local/charmm27/par_all27_prot_na.inp ./

• cp /usr/local/charmm27/top_all27_prot_na.inp ./

• Download the coordinates for Dickerson's dodecamer from PDB [1] and save it on your disk.

• gunzip 1BNA.pdb.gz

• cp 1BNA.pdb ddoc.pdb

• Edit the file ddoc.pdb and remove all lines that do not start with ATOM or TER. Also, retain the final END. Save the modified file which should look like this :

ATOM      5  O5*   C A   1      18.935  34.195  25.617  1.00 64.35      1BNA  67
ATOM      6  C5*   C A   1      19.130  33.921  24.219  1.00 44.69      1BNA  68
ATOM      7  C4*   C A   1      19.961  32.668  24.100  1.00 31.28      1BNA  69
ATOM      8  O4*   C A   1      19.360  31.583  24.852  1.00 37.45      1BNA  70
......
ATOM    493  N2    G B  12      19.208  25.386  26.096  1.00 29.76      1BNA 551
ATOM    494  N3    G B  12      18.350  23.438  27.053  1.00 21.95      1BNA 552
ATOM    495  C4    G B  12      17.231  22.893  27.570  1.00 13.89      1BNA 553
TER     496        G B  12                                              1BNA 554
END                                                                     1BNA 700                                                                     

• rasmol ddoc.pdb to look at it.

• Now it is time to align the axes of inertia of the molecule with the orthogonal frame : prepare a file with the name moleman.csh containing the following :

#!/bin/tcsh -f

#
# This will read a PDB file and rotate/translate it so that
#  1. the centre of gravity will be at the origin
#  2. the axes of inertia will be aligned with the orthogonal frame
#

lx_moleman2 >& moleman.log << eof
/usr/local/xutil/moleman2.lib
REad ddoc.pdb
XYz ALign_inertia_axes
WRite aligned.pdb
quit
eof


exit

• Run it : source moleman.csh. This should create two files : a log file (moleman.log) and the new pdb (aligned.pdb).

• rasmol aligned.pdb and then set axes on (to confirm the changes).

• We need to prepare two pdb files each containing the coordinates of each of the two chains. The simplest approach is :

• cp aligned.pdb A.pdb

• cp aligned.pdb B.pdb

• Edit A.pdb and retain only the A-chain coordinates. Add an END at the end of the file. Repeat for B.pdb. For example, A.pdb should look like this :

ATOM      5  O5*   C A   1     -18.727 -10.552   3.524  1.00 64.35      1BNA  67
ATOM      6  C5*   C A   1     -17.323 -10.651   3.227  1.00 44.69      1BNA  68
ATOM      7  C4*   C A   1     -17.096 -10.088   1.846  1.00 31.28      1BNA  69
.........
ATOM    245  N2    G A  12      18.548   0.358  -2.572  1.00 40.53      1BNA 307
ATOM    246  N3    G A  12      18.570  -1.926  -2.048  1.00 37.34      1BNA 308
ATOM    247  C4    G A  12      18.657  -2.793  -1.013  1.00 31.14      1BNA 309
END   

• Create a file with the name psfgen.csh containing the following (see the NAMD manual for psfgen documentaion. For more details on using psfgen with DNA see [2]) :

#!/bin/tcsh -f

/usr/local/NAMD_2.5/psfgen >& psfgen.log << END
topology top_all27_prot_na.inp

alias residue C CYT
alias residue T THY
alias residue A ADE
alias residue G GUA

alias atom THY O5* O5'
alias atom THY C5* C5'
alias atom THY C4* C4'
alias atom THY O4* O4'
alias atom THY C1* C1'
alias atom THY C2* C2'
alias atom THY C3* C3'
alias atom THY O3* O3'

alias atom GUA O5* O5'
alias atom GUA C5* C5'
alias atom GUA C4* C4'
alias atom GUA O4* O4'
alias atom GUA C1* C1'
alias atom GUA C2* C2'
alias atom GUA C3* C3'
alias atom GUA O3* O3'

alias atom ADE O5* O5'
alias atom ADE C5* C5'
alias atom ADE C4* C4'
alias atom ADE O4* O4'
alias atom ADE C1* C1'
alias atom ADE C2* C2'
alias atom ADE C3* C3'
alias atom ADE O3* O3'

alias atom CYT O5* O5'
alias atom CYT C5* C5'
alias atom CYT C4* C4'
alias atom CYT O4* O4'
alias atom CYT C1* C1'
alias atom CYT C2* C2'
alias atom CYT C3* C3'
alias atom CYT O3* O3'

segment A {
  first 5TER
  last 3TER
  pdb A.pdb
 }

patch DEO2 A:2
patch DEO2 A:4
patch DEO2 A:5
patch DEO2 A:6
patch DEO2 A:10
patch DEO2 A:12

patch DEO1 A:1
patch DEO1 A:3
patch DEO1 A:7
patch DEO1 A:8
patch DEO1 A:9
patch DEO1 A:11


coordpdb A.pdb A


segment B {
  first 5TER
  last 3TER
  pdb B.pdb
 }

patch DEO2 B:2
patch DEO2 B:4
patch DEO2 B:5
patch DEO2 B:6
patch DEO2 B:10
patch DEO2 B:12

patch DEO1 B:1
patch DEO1 B:3
patch DEO1 B:7
patch DEO1 B:8
patch DEO1 B:9
patch DEO1 B:11

coordpdb B.pdb B

guesscoord
writepsf psfgen.psf
writepdb psfgen.pdb

END

exit

• Use it to generate a new pdb file (psfgen.pdb) and the PSF file (psfgen.psf) needed for the steps that follow : source psfgen.csh. Examine the output from the program (file psfgen.log).

• We now need to neutralise the DNA charges. The simple-minded approach (with VMD's autoionize plugin) used for proteins is not satisfactory for DNA : the ions' placement must take into account the DNA's electrostatic field. The best approach would have been to solve the Poisson-Boltzmann equation (with the program Delphi for example) and use the calculated field to guide ion placement. A more simple minded (and less computationally intensive) approach is to start placing the ions one-by-one using a simple Coulomb-based potential. This is implemented with the program sodium, do a less /usr/local/doc/sodium.c to read its documentation. The steps we need to take are :

• Prepare a PDB file containing partial charges on the B-factor column. This you do with a script this time for xplor. Save the following script in a file named xplor.sh, and run it with source xplor.sh.

#!/bin/tcsh -f

xplorbig > xplor.log << eof
structure @psfgen.psf end
coor @psfgen.pdb
vector do (B=CHARGE) (all)
write coor output="psfgen_charges.pdb" end
stop
eof

exit

• Examine the output (file psfgen_charges.pdb) and confirm that the charges are there.

• Prepare a configuration file for sodium with the name sodium.config containing the following :

NUM_IONS      22
R_ION_PRODNA  6.5
R_ION_ION     11.0
GRID_STEP     0.50
BORDER_WIDTH  10.0
PDB_NAME      psfgen_charges.pdb
PDB_OUT       ions.pdb

• Run it sodium < sodium.config > sodium.log. For such a small system it will only take a minute or two.

• Check the sodium.log file, check the ion distribution : cat psfgen.pdb ions.pdb > sodium_test.pdb ; rasmol sodium_test.pdb and then select not DNA, cpk.

• You can experiment by changing the sodium parameters controling either the minimum distance between ions and DNA, or the minimum ion-ion distance. Compare the resulting structures to see how the ions structure changes. How would you choose values for these two parameters ?

• Re-create PDB and PSF files for the system this time including the ions. To do this prepare a file psfgen_ions.sh containing the following :

#!/bin/tcsh -f

/usr/local/NAMD_2.5/psfgen >& psfgen_ions.log << END
topology top_all27_prot_na.inp

alias residue C CYT
alias residue T THY
alias residue A ADE
alias residue G GUA

alias atom THY O5* O5'
alias atom THY C5* C5'
alias atom THY C4* C4'
alias atom THY O4* O4'
alias atom THY C1* C1'
alias atom THY C2* C2'
alias atom THY C3* C3'
alias atom THY O3* O3'

alias atom GUA O5* O5'
alias atom GUA C5* C5'
alias atom GUA C4* C4'
alias atom GUA O4* O4'
alias atom GUA C1* C1'
alias atom GUA C2* C2'
alias atom GUA C3* C3'
alias atom GUA O3* O3'

alias atom ADE O5* O5'
alias atom ADE C5* C5'
alias atom ADE C4* C4'
alias atom ADE O4* O4'
alias atom ADE C1* C1'
alias atom ADE C2* C2'
alias atom ADE C3* C3'
alias atom ADE O3* O3'

alias atom CYT O5* O5'
alias atom CYT C5* C5'
alias atom CYT C4* C4'
alias atom CYT O4* O4'
alias atom CYT C1* C1'
alias atom CYT C2* C2'
alias atom CYT C3* C3'
alias atom CYT O3* O3'

segment A {
  first 5TER
  last 3TER
  pdb A.pdb
 }
patch DEO2 A:2
patch DEO2 A:4
patch DEO2 A:5
patch DEO2 A:6
patch DEO2 A:10
patch DEO2 A:12

patch DEO1 A:1
patch DEO1 A:3
patch DEO1 A:7
patch DEO1 A:8
patch DEO1 A:9
patch DEO1 A:11

coordpdb A.pdb A


segment B {
  first 5TER
  last 3TER
  pdb B.pdb
 }

patch DEO2 B:2
patch DEO2 B:4
patch DEO2 B:5
patch DEO2 B:6
patch DEO2 B:10
patch DEO2 B:12

patch DEO1 B:1
patch DEO1 B:3
patch DEO1 B:7
patch DEO1 B:8
patch DEO1 B:9
patch DEO1 B:11


coordpdb B.pdb B


segment SOD {
  pdb ions.pdb
 }

coordpdb ions.pdb SOD

guesscoord
writepsf psfgen_ions.psf
writepdb psfgen_ions.pdb

END

exit

• Run it with source psfgen_ions.sh, examine log and PDB file.

• Time to hydrate the system : Create a file with the name vmd.script containing the following script (for VMD) :

#
# This is a short script implementing VMD's 'solvate' to prepare 
# a fully solvated system for a periodic boundary simulation. 
# It also prepares two pdb files needed for implementing restrains
# during the heating-up phase.
#

#
# Make water box
#
solvate psfgen_ions.psf psfgen_ions.pdb -o hydrated -b 1.80 -t 15.0

#
# Here you can add additional ions to emulate higher ionic strength
# conditions. In this case we add 50mM salt, increasing the effective
# ionic strength to approximately 250mM.
#
package require autoionize
autoionize -psf hydrated.psf -pdb hydrated.pdb -is 0.050

#
# Prepare restraints files
#
mol load psf ionized.psf pdb ionized.pdb

set all [atomselect top all]
set sel [atomselect top "nucleic and name P"]
$all set beta 0
$sel set beta 0.5
$all writepdb restrain_P.pdb


set all [atomselect top all]
set to_fix [atomselect top "nucleic and backbone"]
$all set beta 0
$to_fix set beta 1
$all writepdb fix_backbone.pdb

• Run this script via VMD :

• Start VMD : vmd

• Locate VMD's console (window with the prompt)

• In the console give source vmd.script

• If all goes well you should see your fully hydrated and ionised system on VMD's graphics window1.

• To finish type quit in the console.

• Use rasmol or vmd to study your system (ionized.pdb). Make sure that there are no waters or ions accidentally placed inside your molecule's hydrophobic core.

• The last step before running NAMD is to determine the limits (along the orthogonal frame) of the system. A fast method to do this is to use the program pdbset from the CCP4 suite of program. Here it is how :

• Start it : pdbset xyzin ionized.pdb >& pdbset.log

• Type END

• Edit the file pdbset.log. Somewhere near the end of it you will see something similar to :

 Orthogonal Coordinate limits in output file:
                 Minimum   Maximum    Centre     Range
       On X :     -37.70     36.29     -0.71     74.00
       On Y :     -29.96     30.01      0.03     59.97
       On Z :     -30.39     29.60     -0.39     60.00

• Note these numbers, especially the range (on x,y,z) and position of centre.

• Create a NAMD minimisation and heating-up script with the name heat.namd containing the following :

#
# Input files
#
structure               ionized.psf
coordinates             ionized.pdb
parameters              par_all27_prot_na.inp
paraTypeCharmm          on

#
# Output files & writing frequency for DCD
# and restart files
#
outputname              output/heat_out
binaryoutput            off
restartname             output/restart
restartfreq             1000
binaryrestart           yes
dcdFile                 output/heat_out.dcd
dcdFreq                 200

#
# Frequencies for logs and the xst file
#
outputEnergies          20
outputTiming            200
xstFreq                 200

#
# Timestep & friends
#
timestep                2.0
stepsPerCycle           8
nonBondedFreq           1
fullElectFrequency      2

#
# Simulation space partitioning
#
switching               on
switchDist              10
cutoff                  12
pairlistdist            13.5

#
# Basic dynamics
#
temperature             0
COMmotion               no
dielectric              1.0
exclude                 scaled1-4
1-4scaling              1.0
rigidbonds              all

#
# Particle Mesh Ewald parameters. 
#
Pme                     on
PmeGridsizeX            80                      # <===== CHANGE ME
PmeGridsizeY            60                      # <===== CHANGE ME
PmeGridsizeZ            60                      # <===== CHANGE ME


#
# Periodic boundary things
#
wrapWater               on
wrapNearest             on

cellBasisVector1        74.00   00.00   00.00   # <===== CHANGE ME
cellBasisVector2        00.00   60.00   00.00   # <===== CHANGE ME
cellBasisVector3        00.00   00.00   60.00   # <===== CHANGE ME
cellOrigin               0.00    0.00    0.00   # <===== CHANGE ME

#
# Fixed atoms for initial heating-up steps
#
fixedAtoms              on
fixedAtomsForces        on
fixedAtomsFile          fix_backbone.pdb
fixedAtomsCol           B

#
# Restrained atoms for initial heating-up steps
#
constraints             on
consRef                 restrain_P.pdb
consKFile               restrain_P.pdb
consKCol                B

#
# Langevin dynamics parameters
#
langevin                on
langevinDamping         10
langevinTemp            320                     # <===== Check me
langevinHydrogen        on

langevinPiston          on
langevinPistonTarget    1.01325
langevinPistonPeriod    200
langevinPistonDecay     100
langevinPistonTemp      320                     # <===== Check me

useGroupPressure        yes


##########################################
# The actual minimisation and heating-up 
# protocol follows. The number of steps
# shown below are too small for a real run
##########################################

#
# run one step to get into scripting mode
#
minimize                0

#
# turn off pressure control until later
#
langevinPiston          off

#
# minimize nonbackbone atoms
#
minimize                400                     ;# <===== CHANGE ME
output                  output/min_fix

#
# min all atoms
#
fixedAtoms              off
minimize                400                     ;# <===== CHANGE ME
output                  output/min_all

#
# heat with Ps restrained
#
set temp 20;
while { $temp < 321 } {                         ;# <===== Check me
langevinTemp            $temp
run                     400                     ;# <===== CHANGE ME
output                  output/heat_P
set temp [expr $temp + 20]                      
}

#
# equilibrate volume with Ps restrained
#
langevinPiston          on
run                     400                     ;# <===== CHANGE ME
output                  output/equil_P

#
# equilibrate volume without restraints
#
constraintScaling       0
run                     2000                    ;# <===== CHANGE ME

• You can now give it a quick try with NAMD just to make sure it starts without problems. To avoid overloading machines that are already busy with real calculations you must review the cluster usage as follows :

• Type mosmon from your terminal. You should see something similar to this

• This graph shows (in real time) the CPU load for each of the nodes that are currently part of the cluster. The horizontal axis shows the various nodes, the vertical axis shows the corresponding load. If all machines are working properly and they are all running the openMosix linux kernel you should see at least 18 nodes (numbered 25700-25716, plus another node with ID 25854). In this case all cluster nodes are running a proper operating system (and can be seen in the mosmon output) and three of these (25708, 25709 and 25710 corresponding to pc08, pc09 and pc10) are idle. So, nodes pc08, pc09 and pc10 are good candidates for performing your tests.

• Type q to stop mosmon and then give qmon (from your terminal). The main Sun Grid Engine GUI window should appear:

• Select "Queue control". This should pop-up the corresponding window :

• Note the small green boxes (indicating that a job is running) on all nodes except pc08, pc09 and pc10. So, it does look like we could use these three machines for the tests. Press 'Done' on the queue control window and then exit in the qmon window.

• As a first test lets run NAMD on a single node, e.g. pc09 : login to it with ssh pc9 (use your password to login). Then cd to the directory containing your file : oops, no such file or directory ? That's right : you created the files on your local machine, which probably isn't pc09. So, here comes the need for a cluster-wide filesystem. This is implemented in the form of the /work directory. Proceed as follows :

• Logout from pc09 : exit

• cd /work

• ls

• cd tmp

• mkdir my_tests

• Now go back to the directory containing the files you created. Of all the files present in there you only need to copy those few :

cp ionized.p* par_all27_prot_na.inp heat.namd fix_backbone.pdb restrain_P.pdb /work/tmp/my_tests/

• ssh pc9 and login again

• cd /work/tmp/my_tests/

• ls and you should see your files (although you are connected to pc9).

• mkdir output will create a subdirectory where the output files from NAMD will be written (during the run).

• Now, go for it : runhome /usr/local/NAMD_2.5/namd2 heat.namd. The runhome command tells the openMosix kernel to run the job on the local machine (not to migrate it away). Once the program performs a couple of minimisation steps stop it with <CTRL-C>. What you should see should be similar to :

Charm++: standalone mode (not using charmrun)
Info: NAMD 2.5 for Linux-i686
Info: 
Info: Please visit http://www.ks.uiuc.edu/Research/namd/
Info: and send feedback or bug reports to namd@ks.uiuc.edu
Info: 
Info: Please cite Kale et al., J. Comp. Phys. 151:283-312 (1999)
Info: in all publications reporting results obtained with NAMD.
Info: 
Info: Based on Charm++/Converse 050612 for net-linux-icc
Info: Built Fri Sep 26 17:33:59 CDT 2003 by jim on lisboa.ks.uiuc.edu
Info: Sending usage information to NAMD developers via UDP.  Sent data is:
Info: 1 NAMD  2.5  Linux-i686  1    aspera.cluster.mbg.gr  glykos
Info: Running on 1 processors.
Info: 1335 kB of memory in use.
Measuring processor speeds... Done.
Info: Configuration file is heat.namd
TCL: Suspending until startup complete.
Info: SIMULATION PARAMETERS:
Info: TIMESTEP               2
Info: NUMBER OF STEPS        0
Info: STEPS PER CYCLE        8
Info: PERIODIC CELL BASIS 1  74 0 0
Info: PERIODIC CELL BASIS 2  0 60 0
Info: PERIODIC CELL BASIS 3  0 0 60
Info: PERIODIC CELL CENTER   0 0 0
Info: WRAPPING WATERS AROUND PERIODIC BOUNDARIES ON OUTPUT.
Info: WRAPPING TO IMAGE NEAREST TO PERIODIC CELL CENTER.
Info: LOAD BALANCE STRATEGY  Other
Info: LDB PERIOD             1600 steps
Info: FIRST LDB TIMESTEP     40
Info: LDB BACKGROUND SCALING 1
Info: HOM BACKGROUND SCALING 1
Info: PME BACKGROUND SCALING 1
Info: MAX SELF PARTITIONS    50
Info: MAX PAIR PARTITIONS    20
Info: SELF PARTITION ATOMS   125
Info: PAIR PARTITION ATOMS   200
Info: PAIR2 PARTITION ATOMS  400
Info: INITIAL TEMPERATURE    0
Info: CENTER OF MASS MOVING? NO
Info: DIELECTRIC             1
Info: EXCLUDE                SCALED ONE-FOUR
Info: 1-4 SCALE FACTOR       1
Info: DCD FILENAME           output/heat_out.dcd
Info: DCD FREQUENCY          200
Warning: INITIAL COORDINATES WILL NOT BE WRITTEN TO DCD FILE
Info: XST FILENAME           output/heat_out.xst
Info: XST FREQUENCY          200
Info: NO VELOCITY DCD OUTPUT
Info: OUTPUT FILENAME        output/heat_out
Info: RESTART FILENAME       output/restart
Info: RESTART FREQUENCY      1000
Info: BINARY RESTART FILES WILL BE USED
Info: SWITCHING ACTIVE
Info: SWITCHING ON           10
Info: SWITCHING OFF          12
Info: PAIRLIST DISTANCE      13.5
Info: PAIRLIST SHRINK RATE   0.01
Info: PAIRLIST GROW RATE     0.01
Info: PAIRLIST TRIGGER       0.3
Info: PAIRLISTS PER CYCLE    2
Info: PAIRLISTS ENABLED
Info: MARGIN                 0.48
Info: HYDROGEN GROUP CUTOFF  2.5
Info: PATCH DIMENSION        16.48
Info: ENERGY OUTPUT STEPS    20
Info: TIMING OUTPUT STEPS    200
Info: FIXED ATOMS ACTIVE
Info: FORCES BETWEEN FIXED ATOMS ARE CALCULATED
Info: HARMONIC CONSTRAINTS ACTIVE
Info: HARMONIC CONS EXP      2
Info: LANGEVIN DYNAMICS ACTIVE
Info: LANGEVIN TEMPERATURE   320
Info: LANGEVIN DAMPING COEFFICIENT IS 10 INVERSE PS
Info: LANGEVIN DYNAMICS APPLIED TO HYDROGENS
Info: LANGEVIN PISTON PRESSURE CONTROL ACTIVE
Info:        TARGET PRESSURE IS 1.01325 BAR
Info:     OSCILLATION PERIOD IS 200 FS
Info:             DECAY TIME IS 100 FS
Info:     PISTON TEMPERATURE IS 320 K
Info:       PRESSURE CONTROL IS GROUP-BASED
Info:    INITIAL STRAIN RATE IS 0 0 0
Info:       CELL FLUCTUATION IS ISOTROPIC
Info: PARTICLE MESH EWALD (PME) ACTIVE
Info: PME TOLERANCE               1e-06
Info: PME EWALD COEFFICIENT       0.257952
Info: PME INTERPOLATION ORDER     4
Info: PME GRID DIMENSIONS         80 60 60
Info: Attempting to read FFTW data from FFTW_NAMD_2.5_Linux-i686.txt
Info: Optimizing 6 FFT steps.  1... 2... 3... 4... 5... 6...   Done.
Info: Writing FFTW data to FFTW_NAMD_2.5_Linux-i686.txt
Info: FULL ELECTROSTATIC EVALUATION FREQUENCY      4
Info: USING VERLET I (r-RESPA) MTS SCHEME.
Info: C1 SPLITTING OF LONG RANGE ELECTROSTATICS
Info: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS
Info: RIGID BONDS TO HYDROGEN : ALL
Info:         ERROR TOLERANCE : 1e-08
Info:          MAX ITERATIONS : 100
Info: RIGID WATER USING SETTLE ALGORITHM
Info: NONBONDED FORCES EVALUATED EVERY 2 STEPS
Info: RANDOM NUMBER SEED     1109584307
Info: USE HYDROGEN BONDS?    NO
Info: COORDINATE PDB         ionized.pdb
Info: STRUCTURE FILE         ionized.psf
Info: PARAMETER file: CHARMM format! 
Info: PARAMETERS             par_all27_prot_na.inp
Info: SUMMARY OF PARAMETERS:
Info: 250 BONDS
Info: 622 ANGLES
Info: 1049 DIHEDRAL
Info: 73 IMPROPER
Info: 130 VDW
Info: 0 VDW_PAIRS
Info: ****************************
Info: STRUCTURE SUMMARY:
Info: 25117 ATOMS
Info: 17038 BONDS
Info: 9599 ANGLES
Info: 2228 DIHEDRALS
Info: 68 IMPROPERS
Info: 0 EXCLUSIONS
Info: 22 CONSTRAINTS
Info: 176 FIXED ATOMS
Info: 24569 RIGID BONDS
Info: 0 RIGID BONDS BETWEEN FIXED ATOMS
Info: 50254 DEGREES OF FREEDOM
Info: 8647 HYDROGEN GROUPS
Info: 108 HYDROGEN GROUPS WITH ALL ATOMS FIXED
Info: TOTAL MASS = 154535 amu
Info: TOTAL CHARGE = 8.23289e-07 e
Info: *****************************
Info: Entering startup phase 0 with 7301 kB of memory in use.
Info: Entering startup phase 1 with 7301 kB of memory in use.
Info: Entering startup phase 2 with 8984 kB of memory in use.
Info: Entering startup phase 3 with 9184 kB of memory in use.
Info: PATCH GRID IS 4 (PERIODIC) BY 3 (PERIODIC) BY 3 (PERIODIC)
Info: REMOVING COM VELOCITY 0 0 0
Info: LARGEST PATCH (5) HAS 760 ATOMS
Info: Entering startup phase 4 with 12394 kB of memory in use.
Info: PME using 1 and 1 processors for FFT and reciprocal sum.
Creating Strategy 4
Creating Strategy 4
Info: PME GRID LOCATIONS: 0
Info: PME TRANS LOCATIONS: 0
Info: Optimizing 4 FFT steps.  1... 2... 3... 4...   Done.
Info: Entering startup phase 5 with 13567 kB of memory in use.
Info: Entering startup phase 6 with 13567 kB of memory in use.
Info: Entering startup phase 7 with 13567 kB of memory in use.
Info: COULOMB TABLE R-SQUARED SPACING: 0.0625
Info: COULOMB TABLE SIZE: 769 POINTS
Info: NONZERO IMPRECISION IN COULOMB TABLE: 2.64698e-22 (712) 2.64698e-22 (712)
Info: NONZERO IMPRECISION IN COULOMB TABLE: 1.26218e-29 (742) 1.57772e-29 (742)
Info: NONZERO IMPRECISION IN COULOMB TABLE: 1.27055e-21 (767) 1.48231e-21 (767)
Info: Entering startup phase 8 with 16909 kB of memory in use.
Info: Finished startup with 21797 kB of memory in use.
TCL: Minimizing for 0 steps
ETITLE:      TS           BOND          ANGLE          DIHED          IMPRP               ELECT            VDW       BOUNDARY           MISC        KINETIC               TOTAL           TEMP         TOTAL2         TOTAL3        TEMPAVG            PRESSURE      GPRESSURE         VOLUME       PRESSAVG      GPRESSAVG

ENERGY:       0      8367.1615      2562.3243       745.3077         0.7495         -86828.1909   2661304.0749         0.0000         0.0000         0.0000        2586151.4269         0.0000   2586151.4269   2586151.4269         0.0000        2770784.8777   2821435.1130    266400.0000   2770784.8777   2821435.1130

TCL: Setting parameter langevinPiston to off
TCL: Minimizing for 400 steps
ETITLE:      TS           BOND          ANGLE          DIHED          IMPRP               ELECT            VDW       BOUNDARY           MISC        KINETIC               TOTAL           TEMP         TOTAL2         TOTAL3        TEMPAVG            PRESSURE      GPRESSURE         VOLUME       PRESSAVG      GPRESSAVG

ENERGY:       0      8367.1615      2562.3243       745.3077         0.7495         -86828.1909   2661304.0749         0.0000         0.0000         0.0000        2586151.4269         0.0000   2586151.4269   2586151.4269         0.0000        2770784.8777   2821435.1130    266400.0000   2770784.8777   2821435.1130

INITIAL STEP: 1e-06
GRADIENT TOLERANCE: 6.07456e+07
ENERGY:       1      8461.3964      2575.7790       745.3495         0.7474         -86744.8887     66834.9357         0.0000         0.0000         0.0000          -8126.6806         0.0000     -8126.6806     -8126.6806         0.0000          62244.7987     65640.3834    266400.0000     62244.7987     65640.3834

ENERGY:       2      8797.5006      2631.6879       745.3945         0.7454         -86710.0767     39177.7886         0.0000         0.0000         0.0000         -35356.9597         0.0000    -35356.9597    -35356.9597         0.0000          33177.5662     35521.3466    266400.0000     33177.5662     35521.3466

ENERGY:       3     10026.8780      2749.8692       745.4941         0.7418         -86681.3159     31642.7422         0.0000         0.0000         0.0000         -41515.5906         0.0000    -41515.5906    -41515.5906         0.0000          24842.4717     28926.6604    266400.0000     24842.4717     28926.6604

ENERGY:       4     16301.5980      3252.9024       745.7321         0.7358         -86621.8424   6474574.1627         0.0000         0.0000         0.0000        6408253.2887         0.0000   6408253.2887   6408253.2887         0.0000        6747235.8916   6748522.4575    266400.0000   6747235.8916   6748522.4575

BRACKET: 6e-06 6.44977e+06 -8.35686e+09 2.51346e+09 1.63163e+09 

• Wouldn't it be great to run NAMD a bit faster ? Say, approximately three times faster ? Isn't it a pity to have pc08 and pc10 filtering the dust in the terminal room ? While you are at /work/tmp/my_tests/ create a file with the name NAMD.sh containing the following :

#!/bin/csh -f
#

#
# The name of the job
#
#$ -N My_test

#
#                       ====> CHANGE ME <====
#
# The parallel environment (mpi_fast) and number of processors (3)
# The options are :   mpi_fast : the 9 new machines
#                     mpi_slow : the 9 older machines
#                     mpich    : all machines on the cluster
# 
#$ -pe mpi_fast 3

#
# The version of MPICH to use, transport protocol & a trick to delete cleanly
# running MPICH jobs ...
#
#$ -v MPIR_HOME=/usr/local/mpich-ssh
#$ -v P4_RSHCOMMAND=rsh
#$ -v MPICH_PROCESS_GROUP=no
#$ -v CONV_RSH=rsh

#
# Nodes that can server as master queues
# 
#$ -masterq pc01.q,pc02.q,pc03.q,pc04.q,pc05.q,pc06.q,pc07.q,pc08.q,pc09.q,pc10.q,pc11.q,pc12.q,pc13.q,pc14.q,pc16.q

#
# Execute from the current working directory ...
#
#$ -cwd

#
# Standard error and output should go into the current working directory ...
#
#$ -e ./
#$ -o ./

#
# Built nodelist file for charmrun
#
echo "Got $NSLOTS slots."
echo "group main" > $TMPDIR/charmlist
awk '{print "host " $1}' $TMPDIR/machines >> $TMPDIR/charmlist
cat $TMPDIR/charmlist

#
#                       ====> CHANGE ME <====
#
# The name of the NAMD script file is defined here (heat.namd) as well as
# the name of the job's log file (LOG)
# 
/usr/local/NAMD_2.5/charmrun /bin/runhome /usr/local/NAMD_2.5/namd2 ++nodelist $TMPDIR/charmlist +p $NSLOTS heat.namd > LOG

• This script is a parallel NAMD job submission script for the Sun Grid Engine. All you have to do is : qsub NAMD.sh (from the /work/tmp/my_tests/ directory). You should see a message containing your job's ID.

• Type qstat : you should see your job and its status changing from qw to t to r.

• Use mosmon to confirm that the previously idle machines are indeed doing something useful.

• Use qmon to review cluster usage, and to see your job in Job Control/Running Jobs.

• tail -f LOG should show you the growing log file from your job.

• Type mknamdplot LOG and then click Draw to see a collection of graphs showing the evolution of quantities like the system's total energy, pressure, temperature, bond and angle energies, … :

• Click Exit to exit.

• The heating-up NAMD job will take 2-3 hours to finish. Let it do so. But if you'd rather not : qdel JobID will kill your job (or you can use the qmon GUI).

• When the job is done review the files that have been created in /work/tmp/my_tests/output/. You should see something like

-rw-rw-r--    1 glykos   glykos    2029503 Oct 30 15:19 equil_P.coor
-rw-rw-r--    1 glykos   glykos    2029502 Oct 30 15:19 equil_P.vel
-rw-rw-r--    1 glykos   glykos        222 Oct 30 15:19 equil_P.xsc
-rw-rw-r--    1 glykos   glykos    2029503 Oct 30 15:16 heat_P.coor
-rw-rw-r--    1 glykos   glykos    2029503 Oct 30 15:13 heat_P.coor.BAK
-rw-rw-r--    1 glykos   glykos    2029502 Oct 30 15:16 heat_P.vel
-rw-rw-r--    1 glykos   glykos    2029502 Oct 30 15:13 heat_P.vel.BAK
-rw-rw-r--    1 glykos   glykos        153 Oct 30 15:16 heat_P.xsc
-rw-rw-r--    1 glykos   glykos        153 Oct 30 15:13 heat_P.xsc.BAK
-rw-rw-r--    1 glykos   glykos    2029503 Oct 30 15:36 heat_out.coor
-rw-r--r--    1 glykos   glykos   14613396 Oct 30 15:36 heat_out.dcd
-rw-rw-r--    1 glykos   glykos    2029502 Oct 30 15:36 heat_out.vel
-rw-rw-r--    1 glykos   glykos        227 Oct 30 15:36 heat_out.xsc
-rw-rw-r--    1 glykos   glykos       3364 Oct 30 15:36 heat_out.xst
-rw-rw-r--    1 glykos   glykos    2029502 Oct 30 14:25 min_all.coor
-rw-rw-r--    1 glykos   glykos    2029501 Oct 30 14:25 min_all.vel
-rw-rw-r--    1 glykos   glykos        152 Oct 30 14:25 min_all.xsc
-rw-rw-r--    1 glykos   glykos    2029502 Oct 30 14:19 min_fix.coor
-rw-rw-r--    1 glykos   glykos    2029501 Oct 30 14:19 min_fix.vel
-rw-rw-r--    1 glykos   glykos        152 Oct 30 14:19 min_fix.xsc
-rw-rw-r--    1 glykos   glykos     608836 Oct 30 15:31 restart.coor
-rw-rw-r--    1 glykos   glykos     608836 Oct 30 15:22 restart.coor.old
-rw-rw-r--    1 glykos   glykos     608836 Oct 30 15:31 restart.vel
-rw-rw-r--    1 glykos   glykos     608836 Oct 30 15:22 restart.vel.old
-rw-rw-r--    1 glykos   glykos        229 Oct 30 15:31 restart.xsc
-rw-rw-r--    1 glykos   glykos        228 Oct 30 15:22 restart.xsc.old

• Play time : from the output/ directory give vmd ../ionized.psf heat_out.dcd

• You can now start preparing the equilibration-production run :

• cd /work/tmp/my_tests/

• mkdir heat

• mv * heat/

• mkdir equi

• cd heat/output

• cp heat_out.coor heat_out.vel heat_out.xsc ../../equi/

• cd ..

• cp ionized.p* par_all27_prot_na.inp ../equi/

• cd ../equi

• mkdir output

• Create a NAMD equilibration script with the name equi.namd containing the following :

#
# Input files
#
structure               ionized.psf
coordinates             heat_out.coor
velocities              heat_out.vel
extendedSystem          heat_out.xsc
parameters              par_all27_prot_na.inp
paraTypeCharmm          on

#
# Output files & writing frequency for DCD
# and restart files
#
outputname              output/equi_out
binaryoutput            off
restartname             output/restart
restartfreq             1000
binaryrestart           yes
dcdFile                 output/equi_out.dcd
dcdFreq                 200

#
# Frequencies for logs and the xst file
#
outputEnergies          20
outputTiming            200
xstFreq                 200

#
# Timestep & friends
#
timestep                2.0
stepsPerCycle           8
nonBondedFreq           1
fullElectFrequency      2

#
# Simulation space partitioning
#
switching               on
switchDist              10
cutoff                  12
pairlistdist            13.5

#
# Basic dynamics
#
COMmotion               no
dielectric              1.0
exclude                 scaled1-4
1-4scaling              1.0
rigidbonds              all

#
# Particle Mesh Ewald parameters. 
#
Pme                     on
PmeGridsizeX            80                      # <===== CHANGE ME
PmeGridsizeY            60                      # <===== CHANGE ME
PmeGridsizeZ            60                      # <===== CHANGE ME


#
# Periodic boundary things
#
wrapWater               on
wrapNearest             on
wrapAll                 on


#
# Langevin dynamics parameters
#
langevin                on
langevinDamping         1
langevinTemp            320                     # <===== Check me
langevinHydrogen        on

langevinPiston          on
langevinPistonTarget    1.01325
langevinPistonPeriod    200
langevinPistonDecay     100
langevinPistonTemp      320                     # <===== Check me

useGroupPressure        yes

firsttimestep           9600                     # <===== CHANGE ME
run                     4000                    ;# <===== CHANGE ME

• Prepare a submission script for SGE, say NAMD.sh :

#!/bin/csh -f
#

#
# The name of the job
#
#$ -N test_equi

#
# The parallel environment (mpi_fast) and number of processors (9) ...
# 
#$ -pe mpi_fast 3

#
# The version of MPICH to use, transport protocol & a trick to delete cleanly
# running MPICH jobs ...
#
#$ -v MPIR_HOME=/usr/local/mpich-ssh
#$ -v P4_RSHCOMMAND=rsh
#$ -v MPICH_PROCESS_GROUP=no
#$ -v CONV_RSH=rsh

#
# Nodes that can server as master queues
# 
#$ -masterq pc01.q,pc02.q,pc03.q,pc04.q,pc05.q,pc06.q,pc07.q,pc08.q,pc09.q,pc10.q,pc11.q,pc12.q,pc13.q,pc14.q,pc16.q

#
# Execute from the current working directory ...
#
#$ -cwd

#
# Standard error and output should go into the current working directory ...
#
#$ -e ./
#$ -o ./

#
# Built nodelist file for charmrun
#
echo "Got $NSLOTS slots."
echo "group main" > $TMPDIR/charmlist
awk '{print "host " $1}' $TMPDIR/machines >> $TMPDIR/charmlist
cat $TMPDIR/charmlist

#
# Ready ...
#
/usr/local/NAMD_2.5/charmrun /bin/runhome /usr/local/NAMD_2.5/namd2 ++nodelist $TMPDIR/charmlist +p $NSLOTS equi.namd > LOG

• Run it : qsub NAMD.sh

• Enjoy.