Running job on clusters continuously

Here is a way to run jobs on cluster in a continuous fashion. This example addresses NAMD jobs but should also work for others.

Extracting coordinates of protein from a simulation

set dir [pwd]
mol new     ${dir}/ache.psf       type {psf}
mol addfile ${dir}/ache.pdb       type {pdb} waitfor all
mol addfile ${dir}/acheminnpt.dcd type {dcd} waitfor all

set molnum 0
set skip 1
set backframe0 [atomselect $molnum backbone frame 0]

for {set i 0} {$i < [molinfo $molnum get numframes]} {incr i $skip} {
set pro  [atomselect $molnum protein  frame $i]

# Change 'protein' to "resid N to Z" to suit your needs.
set back [atomselect $molnum backbone frame $i]
set trans_mat [measure fit $back $backframe0]
$pro move $trans_mat
set k [expr $i/$skip]
$pro writedcd ${dir}/dcd/project-pdb-$k.dcd
}

Now generate a protein-only psf file. At this stage you should have n number of dcd files. To join them all in to one dcd file,

mol new    ${dir}/ache_protein.psf
set pro_frames [expr [molinfo $molnum get numframes]/$skip ]
for {set j 0} {$j < $pro_frames} {incr j 1} {
mol addfile ${dir}/dcd/project-pdb-$j.dcd
}
set top [molinfo top]
animate write dcd {${dir}/dcd/project_protein.dcd} beg 0 end [expr $pro_frames - 1] skip 1 [molinfo top]

The last step is where the individual files are stitched together.

NAMD sample scripts

http://www.ks.uiuc.edu/Research/namd/2.7/ug/node64.html

This file demonstrates the analysis of a DCD trajectory file using NAMD. The file pair.pdb contains the definition of pair interaction groups; NAMD will compute the interaction energy and force between these groups for each frame in the DCD file. It is assumed that coordinate frames were written every 1000 timesteps. See Sec. 12.1 for more about pair interaction calculations.

# initial config
coordinates     alanin.pdb
temperature     0

# output params
outputname      /tmp/alanin-analyze
binaryoutput    no

# integrator params
timestep        1.0

# force field params
structure       alanin.psf
parameters      alanin.params
exclude         scaled1-4
1-4scaling      1.0
switching       on
switchdist      8.0
cutoff          12.0
pairlistdist    13.5
stepspercycle   20
 
# Atoms in group 1 have a 1 in the B column; group 2 has a 2.
pairInteraction  on
pairInteractionFile pair.pdb
pairInteractionCol B
pairInteractionGroup1 1
pairInteractionGroup2 2

# First frame saved was frame 1000.
set ts 1000

coorfile open dcd /tmp/alanin.dcd

# Read all frames until nonzero is returned.
while { ![coorfile read] } {
  # Set firstTimestep so our energy output has the correct TS.
  firstTimestep $ts
  # Compute energies and forces, but don't try to move the atoms.
  run 0
  incr ts 1000
}
coorfile close