Re: efield energies incorrect in analysis mode (run 0) ?

From: Mark Triger (
Date: Thu Jun 28 2012 - 14:22:18 CDT

The main difference between the analysis version of the NAMD script
and the original script used to run it is the removal of elements
related to temperature and pressure control - since there's no
dynamics being performed. Similarly, velocity information is lost,
since the DCD trajectory doesn't cover every timestep of the original
simulation. So the fact that the I don't get back my pressure,
temperature, or kinetic energy seems sensible enough. (I do get back
the same volume).

Can't think of any obvious reason why I should get a different efield
energy though...

I've appended my analysis script.



structure struct.psf
coordinates struct.pdb
temperature 0;

outputname tempfile

binCoordinates equi.coor;
extendedSystem equi.xsc;
paraTypeCharmm on;
parameters toppar/par_all22_prot.prm;

exclude scaled1-4
1-4scaling 1.0
switching on
vdwForceSwitching yes;
cutoff 12.0;
switchdist 10.0;
 pairlistdist 16.0;
stepspercycle 1;
pairlistsPerCycle 1;
timestep 2.0;
rigidBonds all;
nonbondedFreq 1;
fullElectFrequency 1;
wrapWater on;
wrapAll on;
wrapNearest off;

PME yes;
PMEInterpOrder 6;
PMEGridSizeX 100;
PMEGridSizeY 100;
PMEGridSizeZ 100;

efieldon yes
efield 0. 0. 0.0242

set ts 0
coorfile open dcd equi.dcd
# Read all frames until nonzero is returned.
while { ![coorfile read] } {
firstTimestep $ts
run 0
incr ts 1000
 coorfile close

On Thu, Jun 28, 2012 at 12:29 AM, Norman Geist
<> wrote:
> Hi,
> I never used this feature of namd but possibly you should check why your
> volume and pressure energy changed that much. Maybe try to also load the
> velocities that are part of your end energies anyway and should be there
> when you try to reproduce, as I think you didn't loaded them into the run 0
> script as the temp is 0.
> Norman Geist.

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