Re: can I change coordinate before restart?

From: Joshua Adelman (
Date: Tue Apr 21 2009 - 20:50:47 CDT

Unless you are have hacked your own version of NAMD, I don't believe
that you can have a dissociable force-field running, so it is
impossible for you to have had a hydrogen hop from one oxygen to the
other. You can certainly change your psf and pdb file and start a new
simulation from the last frame of your previous simulation, but it
won't really be a continuation of the previous simulation, especially
if you think that group is playing an important role in the dynamics.
I'm not quite sure how to alter the binary restart files (assuming
that you're using the default), but you can probably just run a single
step and dump the output in ascii format to use to restart a new
simulation. Also you will want to check to make sure that moving the
hydrogen isn't going to cause clashes with other atoms. You'll know
pretty quickly if your system blows up.

I'm not sure about the question of 'error'. It really depends on what
you are trying to extract from the simulation and what this
perturbation does to your system.


On Apr 21, 2009, at 2:03 PM, Mark M Huntress wrote:

> There are 2 different likely positions for a H on a carboxylic group
> in my protein, but I think one is more likely than the other. I have
> run 6 ns with the H in the unlikely position (it hasn't shifted) but
> I think I would like to move it before I restart my simulation. Can
> I just go into the .coor file and move it to the place I want it? Or
> does this introduce inconsistencies- (now the velocity for the H in
> the restart.vel file will not make sense). Is this OK? Will I
> introduce an error or something if I try this?
> Thanks.
> Mark

Joshua L. Adelman
Biophysics Graduate Group Lab: 510.643.2159
218 Wellman Hall Fax: 510.642.7428
University of California, Berkeley
Berkeley, CA 94720 USA

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