MBG wiki: Running a molecular dynamics simulation of native Rop

What follows is a mostly complete description of the practical steps required for performing a short molecular dynamics simulation of a homodimeric protein. Please do keep in mind the difference between doing things, and understanding things.

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 Rop dimer from PDB [1] and save it on your disk. To find the PDB file containing the dimer coordinates search for biological assembly (use 'SHIFT+left mouse click' from netscape to save the compressed file).

gunzip 1rop.pdb1.gz

mv 1rop.pdb1 dimer.pdb

Edit the file dimer.pdb and remove all lines that do not start with ATOM or TER. Also, retain the final END. Now the difficult part : although the file contains two chains, these have the same identifier ' A '. You should find the beginning of the second chain and then use find-and-replace (or use a macro) to change only for the second chain all occurences of the chain identifier ' A ' to ' B '. Save the modified file which should look like this :

ATOM      1  N   MET A   1      31.007   2.290  18.034  1.00 28.97           N  
ATOM      2  CA  MET A   1      32.390   2.582  17.546  1.00 26.82           C  
ATOM      3  C   MET A   1      32.808   1.432  16.618  1.00 21.98           C  
ATOM      4  O   MET A   1      32.375   0.280  16.846  1.00 23.60           O  
......................
ATOM    445  CE1 PHE A  56      38.342   8.335  16.790  1.00 25.49           C  
ATOM    446  CE2 PHE A  56      39.530   7.284  18.653  1.00 23.77           C  
ATOM    447  CZ  PHE A  56      39.527   7.962  17.421  1.00 24.84           C  
TER     448      PHE A  56                                                      
ATOM      1  N   MET B   1      74.680   2.290  35.339  1.00 28.97           N  
ATOM      2  CA  MET B   1      73.297   2.582  35.827  1.00 26.82           C  
ATOM      3  C   MET B   1      72.879   1.432  36.755  1.00 21.98           C  
ATOM      4  O   MET B   1      73.312   0.280  36.526  1.00 23.60           O  
......................
ATOM    446  CE2 PHE B  56      66.157   7.284  34.719  1.00 23.77           C  
ATOM    447  CZ  PHE B  56      66.160   7.962  35.952  1.00 24.84           C  
TER     448      PHE B  56                                                      
END

rasmol dimer.pdb (you should see the Rop dimer).

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 dimer.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 (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. Find-and-replace 'HIS' with 'HSP' (fully protonated histidines, corresponding to performing a run at pH < 61). Save the file. Repeat for B.pdb. For example, A.pdb should look like this :

ATOM      1  N   MET A   1      22.545  -6.589   6.155  1.00 28.97           N
ATOM      2  CA  MET A   1      21.754  -5.355   5.863  1.00 26.82           C
ATOM      3  C   MET A   1      21.994  -4.366   7.013  1.00 21.98           C
......................
ATOM    445  CE1 PHE A  56      17.522  -1.101   0.110  1.00 25.49           C
ATOM    446  CE2 PHE A  56      15.440  -1.841   1.161  1.00 23.77           C
ATOM    447  CZ  PHE A  56      16.199  -0.871   0.483  1.00 24.84           C
END

Create a file with the name psfgen.csh containing the following :

#!/bin/tcsh -f

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

segment A {
 pdb A.pdb
 }
alias atom ILE CD1 CD
coordpdb A.pdb A


segment B {
 pdb B.pdb
 }
alias atom ILE CD1 CD
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 NAMD : source psfgen.csh. Examine the output from the program (file psfgen.log).

Create a file with the name make_all.vmd containing the following script (for VMD) :


#
# This is a short script implementing VMD's 'solvate' and 
# 'autoionize' to prepare a fully solvated and neutral
# 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.psf psfgen.pdb -o hydrated -b 1.80 -t 15.0

#
# Add ions to neutralise charge
#
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 "protein and name CA"]
$all set beta 0
$sel set beta 0.5
$all writepdb restrain_ca.pdb


set all [atomselect top all]
set to_fix [atomselect top "protein 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 make_all.vmd

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

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. If there are, you will have to think : Is there a cavity there ? Would it be possible that there is indeed a water molecule placed in that cavity ? Is there experimental evidence concerning the presence of these waters ? If you do not do that you may end-up with questionable situations like this one :

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 :     -39.30     39.30      0.00     78.60
       On Y :     -30.05     30.05      0.00     60.10
       On Z :     -25.98     30.85      2.44     56.83

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           2
fullElectFrequency      4

#
# 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            64                      # <===== CHANGE ME
PmeGridsizeZ            60                      # <===== CHANGE ME


#
# Periodic boundary things
#
wrapWater               on
wrapNearest             on

cellBasisVector1        78.60   00.00   00.00   # <===== CHANGE ME
cellBasisVector2        00.00   60.10   00.00   # <===== CHANGE ME
cellBasisVector3        00.00   00.00   56.83   # <===== CHANGE ME
cellOrigin               0.00    0.00    2.44   # <===== 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_ca.pdb
consKFile               restrain_ca.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 CAs restrained
#
set temp 20;
while { $temp < 321 } {                         ;# <===== Check me
langevinTemp            $temp
run                     400                     ;# <===== CHANGE ME
output                  output/heat_ca
set temp [expr $temp + 20]                      
}

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

#
# 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

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_ca.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    pc09.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  79.6 0 0
Info: PERIODIC CELL BASIS 2  0 61.1 0
Info: PERIODIC CELL BASIS 3  0 0 57.83
Info: PERIODIC CELL CENTER   0 0 2.44
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 64 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     1099129124
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: 25368 ATOMS
Info: 17518 BONDS
Info: 11126 ANGLES
Info: 4764 DIHEDRALS
Info: 308 IMPROPERS
Info: 0 EXCLUSIONS
Info: 112 CONSTRAINTS
Info: 450 FIXED ATOMS
Info: 24450 RIGID BONDS
Info: 0 RIGID BONDS BETWEEN FIXED ATOMS
Info: 50304 DEGREES OF FREEDOM
Info: 8768 HYDROGEN GROUPS
Info: 226 HYDROGEN GROUPS WITH ALL ATOMS FIXED
Info: TOTAL MASS = 154680 amu
Info: TOTAL CHARGE = 1.60187e-06 e
Info: *****************************
Info: Entering startup phase 0 with 7505 kB of memory in use.
Info: Entering startup phase 1 with 7505 kB of memory in use.
Info: Entering startup phase 2 with 9341 kB of memory in use.
Info: Entering startup phase 3 with 9541 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 (17) HAS 822 ATOMS
Info: Entering startup phase 4 with 12754 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 14006 kB of memory in use.
Info: Entering startup phase 6 with 14006 kB of memory in use.
Info: Entering startup phase 7 with 14006 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 17392 kB of memory in use.
Info: Finished startup with 22280 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      7954.7376      5748.6073       437.1674        41.0044         -82921.4480     14265.3625         0.0000         0.0000         0.0000         -54474.5687         0.0000    -54474.5687    -54474.5687         0.0000           5922.6194      7853.0443    281259.6748      5922.6194      7853.0443

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      7954.7376      5748.6073       437.1674        41.0044         -82921.4480     14265.3625         0.0000         0.0000         0.0000         -54474.5687         0.0000    -54474.5687    -54474.5687         0.0000           5922.6194      7853.0443    281259.6748      5922.6194      7853.0443

INITIAL STEP: 1e-06
GRADIENT TOLERANCE: 28662.8
ENERGY:       1      7935.4448      5745.3453       437.0249        40.9796         -82926.1450     14017.9693         0.0000         0.0000         0.0000         -54749.3812         0.0000    -54749.3812    -54749.3812         0.0000           5666.8255      7600.7423    281259.6748      5666.8255      7600.7423

ENERGY:       2      7916.2985      5742.1035       436.8822        40.9549         -82930.8147     13791.9735         0.0000         0.0000         0.0000         -55002.6022         0.0000    -55002.6022    -55002.6022         0.0000           5432.3391      7370.3167    281259.6748      5432.3391      7370.3167

ENERGY:       3      7878.4431      5735.6817       436.5970        40.9058         -82940.0682     13393.6985         0.0000         0.0000         0.0000         -55454.7421         0.0000    -55454.7421    -55454.7421         0.0000           5016.8834      6964.2358    281259.6748      5016.8834      6964.2358

ENERGY:       4      7804.4690      5723.0900       436.0305        40.8087         -82958.2742     12757.4610         0.0000         0.0000         0.0000         -56196.4151         0.0000    -56196.4151    -56196.4151         0.0000           4345.9939      6314.8795    281259.6748      4345.9939      6314.8795

ENERGY:       5      7663.3786      5698.9262       434.9535        40.6193         -82993.6089     11864.4871         0.0000         0.0000         0.0000         -57291.2443         0.0000    -57291.2443    -57291.2443         0.0000           3384.6148      5398.6693    281259.6748      3384.6148      5398.6693

ENERGY:       6      7408.1034      5654.2007       433.5232        40.2601         -83060.8871     10739.2295         0.0000         0.0000         0.0000         -58785.5701         0.0000    -58785.5701    -58785.5701         0.0000           2131.4370      4224.4109    281259.6748      2131.4370      4224.4109

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_ca.coor
-rw-rw-r--    1 glykos   glykos    2029502 Oct 30 15:19 equil_ca.vel
-rw-rw-r--    1 glykos   glykos        222 Oct 30 15:19 equil_ca.xsc
-rw-rw-r--    1 glykos   glykos    2029503 Oct 30 15:16 heat_ca.coor
-rw-rw-r--    1 glykos   glykos    2029503 Oct 30 15:13 heat_ca.coor.BAK
-rw-rw-r--    1 glykos   glykos    2029502 Oct 30 15:16 heat_ca.vel
-rw-rw-r--    1 glykos   glykos    2029502 Oct 30 15:13 heat_ca.vel.BAK
-rw-rw-r--    1 glykos   glykos        153 Oct 30 15:16 heat_ca.xsc
-rw-rw-r--    1 glykos   glykos        153 Oct 30 15:13 heat_ca.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           2
fullElectFrequency      4

#
# 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            64                      # <===== 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.

Footnotes:

1. For a run at neutral pH HIS should be replaced with either HSE or HSD depending on whether the histidine should be protonated on the δ or ε atoms. This may be determined from the hydrogen-bonding pattern of the histidine (in the context of the structure)