[gmx-developers] possible interplay between intermolecular restraints and parallelization?

Berk Hess hess at kth.se
Tue Mar 18 08:58:56 CET 2014


What do you mean with "special" bonds, angles and dihedrals? Are these 
potentials you coded yourself?
I assume that with "stability problems" you mean that things are 
unstable, not that the simulation stops with a fatal error because it 
can't find atoms in interactions.

If you are using the velocity verlet integrator with inter charge-group 
constraints, that can give issues in parallel. I just uploaded a fix to 
gerrit for release-4-6.



On 03/18/2014 07:04 AM, Erik Lindahl wrote:
> Hi David,
> It's virtually impossible to say without a specific example, but of 
> course things should work fine in parallel too.
> Create a redline and upload a specific example where you get different 
> results or a stability issue and describe the _exact_ conditions so it 
> can be reproduced.
> Cheers,
> Erik
> -- 
> Erik Lindahl <erik.lindahl at scilifelab.se 
> <mailto:erik.lindahl at scilifelab.se>>
> Professor of Biophysics
> Science for Life Laboratory
> Stockholm University & KTH
> Office (SciLifeLab): +46 8 524 81567
> Cell (Sweden): +46 73 4618050
> Cell (US): 1 267 307 8746
> On Mar 17, 2014, at 6:51 PM, David Mobley <dmobley at gmail.com 
> <mailto:dmobley at gmail.com>> wrote:
>> Dear Devs,
>> For many years we have been doing binding free energy calculations 
>> with restraints to hold the ligand in the binding site. Lately, 
>> however, as we move to bigger systems, we simply can't get these 
>> simulations to run stably. Does anyone have experience with using 
>> restraints between relatively distant atoms in parallel simulations? 
>> Any encounters with similar problems or suggestions?
>> Specifically, we normally use a set of six restraints between the 
>> ligand and the protein to restrain the six rigid-body degrees of 
>> freedom. These use three reference atoms in the protein and three in 
>> the ligand, as described in the reference below. Normally these atoms 
>> are relatively distant from one another, by design.
>> We have in the past mostly used distance_restraints, angle_restraints 
>> and dihedral_restraints for implementing these. However, these seem 
>> to lead to stability problems when we run on a few cores (perhaps 8) 
>> as we move to larger systems, and especially so when using 
>> constraints on bonds involving hydrogen. Additionally, since these 
>> restraints cannot be applied between 'molecules' in the topology, 
>> this means there are technical reasons we prefer another form for the 
>> restraints.
>> Lately, we have been testing using special bonds, angles, and 
>> dihedrals for restraints between these atoms. However, we keep 
>> encountering stability problems there as well, at least when running 
>> in parallel (we are testing whether running on a single core will 
>> alleviate these). We DO already know that if we take a topology file 
>> which will run stably in serial with the old form of restraints, 
>> convert the restraints to the new form (bonds, angles, dihedrals) and 
>> attempt to run it in parallel we tend to run into problems.
>> In any case, does anyone have experience with using restraints 
>> between relatively distant atoms, and suggestions on how to get our 
>> systems to run stably? For what it's worth, these are systems which 
>> run fine in parallel without the restraints, and the restraints are 
>> not unusually strong. (We've run with stronger restraints many times 
>> in the past without issues).
>> Thanks!
>> Reference:
>> http://dx.doi.org/10.1021/jp0217839
>> -- 
>> David Mobley
>> dmobley at gmail.com <mailto:dmobley at gmail.com>
>> 949-385-2436
>> -- 
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