Hi Ross,
Thanks for the suggestion.
>>> Try explicitly setting nscm=0 in the cntrl namelist and see if this helps. You can't use nscm with langevin and restraints. NSCM 'should' be set to zero automatically if you use restraints but I am not sure if this is in AMBER 11 or not and the default for NSCM is 1000.
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 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.
Thanks!
Aysegul
________________________________________
From: Ross Walker [ross.rosswalker.co.uk]
Sent: Monday, August 22, 2011 1:33 PM
To: 'AMBER Mailing List'
Subject: Re: [AMBER] Using iwrap with harmonic restraints
Hi Aysegul
> So I turned off iwrap keeping everything else the same, assuming a
> restrained molecule will not be diffusing much without any problems in
> the restraint energy. However, at the end of each restart, the molecule
> is translated (I can see in VMD that the coordinates at the end the
> first restart and at the start of the second one are not the same). And
> when I restart after 250 psec, the restraint energy increases
> significantly from the last step of the previous restart (1.0082) to
> the first step of the current restart (112371.5346). At the beginning
> of the 3rd restart, every more strangely, the substrate is separated
> from the enzyme (I don’t think it’s simply diffusion because it’s still
> bound tightly at the end of the 2nd restart). The restraint is not only
> on the substrate by the way, both substrate and the a few residues of
> the binding site is restrained. On the other hand, when I restart at
> every 1ns, during the first 1 ns everything’s fine (coordinates and
> energies) but the second rst won’t start.
Try explicitly setting nscm=0 in the cntrl namelist and see if this helps. You can't use nscm with langevin and restraints. NSCM 'should' be set to zero automatically if you use restraints but I am not sure if this is in AMBER 11 or not and the default for NSCM is 1000.
> I thought because I set ig=-1 (for Langevin thermostat), could I
> actually be assigning new velocities at each restart? But it shouldn’t
It will only do this if you are NOT setting irest=1 so this is fine.
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.
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 Mon Aug 22 2011 - 17:30:03 PDT
