Re: can I change coordinate before restart?

From: Joshua Adelman (
Date: Wed Apr 22 2009 - 15:11:55 CDT

Hi Mark,

You can try moving the H manually and see what happens, although it's
always a little dicey to apply what you 'think' should be happening to
a simulation. I guess there are two possibilities:
1. The system was setup in such a way that the hydrogen position found
it's way into a local minimum, and the barrier to flip into the other
position is relatively large such that on the time scales you're
simulating it never gets an excitation that allows it to flip to the
new position (which is also stable).
2. The H position you want to try is high enough energy that it
doesn't want to be there relative to it's current position.

I have never gone in and hand-tuned atom positions, so I don't have
any experience with this. Others might have better advice.


PS - make sure you cc the namd-l list on responses (i.e. keep
discussions on list), because others might have similar questions in
the future and might benefit from the discussions (if they bother to
search the archive before they post a question to the list).

On Apr 22, 2009, at 12:19 PM, Mark M Huntress wrote:

> Joshua,
> Oh, sorry, I don't mean switching the H from one O to the other, I
> just mean to point it out instead of up. I have run MD on very
> similar proteins, and this H doesn't really ever move from the
> position I start it at (does this sound strange to you?), but I
> think I want it to point out, because if it is pointing up, the H is
> closer to a positively charged group.
> And my .coor file is not in binary, so I figured I could just just
> change it in that file, because that is the file I am using for
> coordinates when I restart. Does that sound like it would work?
> Thanks,
> Mark
> ________________________________________
> From: Joshua Adelman []
> Sent: Tuesday, April 21, 2009 9:50 PM
> To: Mark M Huntress
> Cc:
> Subject: Re: namd-l: can I change coordinate before restart?
> 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.
> Josh
> 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
> ------------------------------------------------------------------------------------------------------

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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