From: Nielsen, Steven (steven.nielsen_at_utdallas.edu)
Date: Thu Nov 01 2018 - 12:30:21 CDT
Clever use of namdenergy will do it. You would run a full simulation and then feed the trajectory (dcd) file to a tcl script invoking the namdenergy command.
-Steve
On Nov 1, 2018, at 11:46 AM, Asghar Razavi <asr2013_at_med.cornell.edu<mailto:asr2013_at_med.cornell.edu>> wrote:
Dear all,
It is my understanding that to calculate pair interaction energies you would need to create a pdb file that specifies which atoms need to be used for energy calculations. If I want to calculate interaction energies for e.g. 100 pairs, I would need 100 pdb files.
Instead of creating 100 NAMD input files and invoking NAMD 100 times, I have been trying to adjust the following script to automatically load each pdb file and do the calculations. However, I get the error:
TCL: Setting parameter coordinates to C_10_15.pdb
FATAL ERROR: Setting parameter coordinates from script failed!
I have noticed that other people in the past have been experiencing similar problems when trying to automate the procedure. Does anyone have a better/faster way of doing these calculations or know how to adjust the following script to make calculations automated?
Thank you very much,
Asghar
structure wt.psf
paraTypeCharmm on
parameters par_all36_prot.prm
parameters par_all36_lipid.prm
parameters par_water_ions.prm
numsteps 1
exclude scaled1-4
outputname namd-temp
temperature 0
COMmotion yes
cutoff 12
dielectric 1.0
switchdist 10
pairInteraction on
pairInteractionGroup1 1
pairInteractionGroup2 2
pairInteractionSelf off
for {set i 14} {$i < 18} {incr i} {
coordinates C_10_$i.pdb
pairInteractionFile C_10_$i.pdb
coorfile open dcd tmp_10.dcd
set ts 0
while { ![coorfile read] } {
firstTimestep $ts
run 0
incr ts 1
}
coorfile close
}
-----------------------------------------------
Asghar Razavi
Postdoctoral Associate
Department of Physiology and Biophysics
Weill Cornell Medical College (WCMC)
1300 York Avenue, Room C505
New York, NY 10065<http://maps.google.com/maps?z=16&q=1300+york+avenue,+room+c503+new+york,+ny+10065>
Email: asr2013_at_med.cornell.edu<mailto:asr2013_at_med.cornell.edu>
Website: <http://physiology.med.cornell.edu/faculty/hweinstein/index.html> https://asgharrazavi.net
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