MBG wiki | RecentChanges | Blog | 2021-09-24 | 2021-09-23

Running a molecular dynamics simulation of protein G in a hexagonal cell

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


ATOM      1  N   MET A   1      12.969  18.506  30.954  1.00 15.93      1PGB  70
ATOM      2  CA  MET A   1      13.935  18.529  29.843  1.00 17.40      1PGB  71
ATOM      3  C   MET A   1      13.138  18.692  28.517  1.00 14.65      1PGB  72
ATOM      4  O   MET A   1      12.007  18.222  28.397  1.00 13.04      1PGB  73
ATOM      5  CB  MET A   1      14.733  17.216  29.882  1.00 20.72      1PGB  74
.....
ATOM    434  OE1 GLU A  56       2.544  10.440   6.499  1.00 18.16      1PGB 503
ATOM    435  OE2 GLU A  56       1.737   8.791   7.641  1.00 20.42      1PGB 504
ATOM    436  OXT GLU A  56       6.410   6.617   4.667  1.00 24.74      1PGB 505
TER     437      GLU A  56                                              1PGB 506
END

#!/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 proteinG.pdb
XYz ALign_inertia_axes
WRite aligned.pdb
quit
eof


exit

#!/bin/tcsh -f

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

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


guesscoord
writepsf psfgen.psf
writepdb psfgen.pdb

END

exit

#
# 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
#
package require hexsolvate
hexsolvate psfgen.psf psfgen.pdb -o hydrated -b 1.80 -t 10.0


#
# Add ions to neutralise charge
#
package require autoionize
autoionize -psf hydrated.psf -pdb hydrated.pdb -is 0.150

#
# 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

 Orthogonal Coordinate limits in output file:
                 Minimum   Maximum    Centre     Range
       On X :     -29.05     26.71     -1.17     55.77
       On Y :     -23.36     23.63      0.14     46.98
       On Z :     -20.69     20.61     -0.04     41.29
Do write down these numbers, especially the range (on x,y,z) and position of centre.

#
# 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              8
cutoff                  9
pairlistdist            9.5

#
# 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            54                      # <===== CHANGE ME
PmeGridsizeY            40                      # <===== CHANGE ME
PmeGridsizeZ            40                      # <===== CHANGE ME


#
# Periodic boundary things
#
wrapWater               on
wrapNearest             on

cellBasisVector1        55.77   00.00   00.00   # <===== CHANGE ME
cellBasisVector2        00.00   35.77   20.65   # <===== CHANGE ME
cellBasisVector3        00.00   00.00   41.30   # <===== CHANGE ME
cellOrigin              -1.10    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_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

 Mosmon, three idle nodes

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.

 SGE qmon main window

 SGE qmon qcontrol window

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

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  2    aspera.cluster.mbg.gr  glykos
Info: Running on 2 processors.
Info: 1469 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  55.77 0 0
Info: PERIODIC CELL BASIS 2  0 35.77 20.65
Info: PERIODIC CELL BASIS 3  0 0 41.3
Info: PERIODIC CELL CENTER   -1.1 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           8
Info: SWITCHING OFF          9
Info: PAIRLIST DISTANCE      9.5
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                 0.36
Info: HYDROGEN GROUP CUTOFF  2.5
Info: PATCH DIMENSION        12.36
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       0.348832
Info: PME INTERPOLATION ORDER     4
Info: PME GRID DIMENSIONS         54 40 40
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     1120210498
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: 7395 ATOMS
Info: 5217 BONDS
Info: 3729 ANGLES
Info: 2262 DIHEDRALS
Info: 137 IMPROPERS
Info: 0 EXCLUSIONS
Info: 56 CONSTRAINTS
Info: 225 FIXED ATOMS
Info: 6953 RIGID BONDS
Info: 0 RIGID BONDS BETWEEN FIXED ATOMS
Info: 14557 DEGREES OF FREEDOM
Info: 2620 HYDROGEN GROUPS
Info: 113 HYDROGEN GROUPS WITH ALL ATOMS FIXED
Info: TOTAL MASS = 45579.7 amu
Info: TOTAL CHARGE = 6.35162e-07 e
Info: *****************************
Info: Entering startup phase 0 with 3369 kB of memory in use.
Info: Entering startup phase 1 with 3369 kB of memory in use.
Info: Entering startup phase 2 with 3960 kB of memory in use.
Info: Entering startup phase 3 with 4018 kB of memory in use.
Info: PATCH GRID IS 4 (PERIODIC) BY 2 (PERIODIC) BY 2 (PERIODIC)
Info: REMOVING COM VELOCITY 0 0 0
Info: LARGEST PATCH (10) HAS 513 ATOMS
Info: Entering startup phase 4 with 4970 kB of memory in use.
Info: PME using 2 and 2 processors for FFT and reciprocal sum.
Creating Strategy 4
Creating Strategy 4
Info: PME GRID LOCATIONS: 0 1
Info: PME TRANS LOCATIONS: 0 1
Info: Optimizing 4 FFT steps.  1... 2... 3... 4...   Done.
Info: Entering startup phase 5 with 5337 kB of memory in use.
Info: Entering startup phase 6 with 4891 kB of memory in use.
Info: Entering startup phase 7 with 4897 kB of memory in use.
Info: COULOMB TABLE R-SQUARED SPACING: 0.0625
Info: COULOMB TABLE SIZE: 705 POINTS
Info: NONZERO IMPRECISION IN COULOMB TABLE: 1.58819e-22 (657) 3.17637e-22 (657)
Info: NONZERO IMPRECISION IN COULOMB TABLE: 2.42338e-27 (687) 5.65455e-27 (687)
Info: NONZERO IMPRECISION IN COULOMB TABLE: 1.01644e-20 (700) 2.71051e-20 (700)
Info: Entering startup phase 8 with 6088 kB of memory in use.
Info: Finished startup with 7277 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      2136.4472       642.7569       252.5952        14.1131         -20870.1665  99999999.9999         0.0000         0.0000         0.0000       99999999.9999         0.0000  99999999.9999  99999999.9999         0.0000       99999999.9999  99999999.9999     82389.0768  99999999.9999  99999999.9999

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      2136.4472       642.7569       252.5952        14.1131         -20870.1665  99999999.9999         0.0000         0.0000         0.0000       99999999.9999         0.0000  99999999.9999  99999999.9999         0.0000       99999999.9999  99999999.9999     82389.0768  99999999.9999  99999999.9999

INITIAL STEP: 1e-06
GRADIENT TOLERANCE: 4.66469e+07
ENERGY:       1      2216.6582       646.2796       252.5886        14.1129         -21040.4570    363518.9081         0.0000         0.0000         0.0000         345608.0905         0.0000    345608.0905    345608.0905         0.0000        1220671.1003   1228509.5061     82389.0768   1220671.1003   1228509.5061

ENERGY:       2      2497.3478       656.4725       252.5821        14.1128         -21082.9261     15993.8346         0.0000         0.0000         0.0000          -1668.5763         0.0000     -1668.5763     -1668.5763         0.0000          46937.6944     51815.2083     82389.0768     46937.6944     51815.2083

#!/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 server.q,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

 mknamdplot example

-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

#
# 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              8
cutoff                  9
pairlistdist            9.5

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

#
# Particle Mesh Ewald parameters. 
#
Pme                     on
PmeGridsizeX            54                      # <===== CHANGE ME
PmeGridsizeY            40                      # <===== CHANGE ME
PmeGridsizeZ            40                      # <===== 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                     10000                  ;# <===== CHANGE ME


#!/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 server.q,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