I found an answer to my question in an old post. Sorry for the repeat..
http://structbio.vanderbilt.edu/archives/amber-archive/2008/4467.php
________________________________________
From: Ozen, Aysegul [Aysegul.Ozen.umassmed.edu]
Sent: Tuesday, August 23, 2011 10:38 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Using iwrap with harmonic restraints
Hi Ross,
I finally understood your point and updating the refc at each restart with nscm=0 is working for me now. I have one last question though. To make sure that I‘m not deviating from the initial structure too much, should I have small interval restarts (assuming box size wouldn’t change drastically) or longer restarts (assuming updating refc less number of times would less likely cause large deviation from the initial structure)?
Thanks much!
Aysegul
________________________________________
From: Ross Walker [ross.rosswalker.co.uk]
Sent: Monday, August 22, 2011 9:30 PM
To: 'AMBER Mailing List'
Subject: Re: [AMBER] Using iwrap with harmonic restraints
Hi Aysegul,
> Following your suggestion, I just started another run with explicitly
> setting nscm=0 just to see if it works and it's still running (you're
> right, the default is 1000 in Amber 10). But I'm not optimistic because
> earlier, I had set up another run that's just 100 steps of dt=0.002.
> Because the default was nscm=1000, in a 100 step simulation, COM
> shouldn't have moved (correct?), yet restart messed up the restraint
> energies (I attached the mdout files for the 1st and 2nd rsts). Also
> as I mentioned, an uninterrupted 1 ns run (500000 steps of dt=0.002
> again with the default nscm=1000) seemed just fine in terms of both
> coordinates and energies and if nscm=1000 is what's messing things up,
> then why wouldn't it do so in a 500000 step-run?
If you are using AMBER 10 then I think this will definitely be a problem.
You should always set nscm = 0 if you are doing langevin with restraints.
The problem is that with ntt=3 each nscm trigger shifts the origin but the
restraints are not updated for this and it can cause all sorts of weird
artefacts. AMBER 11 should set nscm=0 for you automatically I believe, but
not AMBER 10.
> >>> If you point the reference coordinates to the previous restart file
> in each case (i.e. always setting refc to the same a -c) then does it
> work? - I know there have been issues with use restraints with NPT
> simulations where the box could change size and this is dealt with
> correctly if you keep using the original structure for the restraints.
>
> REFC is the same equilibrated structure in each restart. So that
> shouldn't be the problem in this case.
But this is my exact point (2). You are running constant pressure I assume
which means that the box size is changing during the simulation as the atom
positions are scaled for each pressure change. Thus the box size when you
restart your simulation does not match the box size of the atoms you are
using for restraints. This causes the restraints to not just try to restrain
the atoms but also fight against the barostat. I know this problem used to
exist but I don't if or when it was ever fixed. I assumed it had been but
what you are reporting looks exactly like this problem. Specifically for NPT
runs the following will work:
sander -O -i mdin.1 -o mdout.1 -p prmtop -x mdcrd.1 -r restrt.1 -c inpcrd
-ref inpcrd
sander -O -I mdin.2 -o mdout.2 -p prmtop -x mdcrd.2 -r restrt.2 -c restrt.1
-ref restrt.1
But the following will NOT work if you are running NPT - it will work fine
for NVT:
sander -O -i mdin.1 -o mdout.1 -p prmtop -x mdcrd.1 -r restrt.1 -c inpcrd
-ref inpcrd
sander -O -I mdin.2 -o mdout.2 -p prmtop -x mdcrd.2 -r restrt.2 -c restrt.1
-ref inpcrd
Hope this helps.
All the best
Ross
/\
\/
|\oss Walker
---------------------------------------------------------
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
|
http://www.rosswalker.co.uk |
http://www.wmd-lab.org/ |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
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Received on Tue Aug 23 2011 - 08:00:04 PDT
