[gmx-users] Packmol starting .pdb and proper equilibration

Justin Lemkul jalemkul at vt.edu
Thu Oct 30 13:14:51 CET 2014

On 10/30/14 7:30 AM, Ioanna Styliari wrote:
> Thank you both for your prompt replies.
> Dr Vitaly Chaban: Is there any way of evaluating how many nodes are needed or is it just by a trial-error approach?

If what Vitaly says is true, this would be a very sneaky bug that has not been 
noticed before.  Of course, if there is a test case that shows this problem, 
it's worth looking at.  But from what I've seen, if the model fails, it will 
eventually fail regardless of the setup.  Drastic differences in forces 
depending on parallelization would be very concerning.

> Justin: Although 1fs works, I was aiming for 2fs steps in the MD but it crashes. I was thinking to run the first 2ns with 1fs and then try to continue it with 2fs onwards to see what happens, but it crashed at 700ps of my MD. I am using GROMOS96 53a6.
> My equilibration "concern" regards the system: should it be equilibrated as a whole or should I equilibrate one part of it at a time, keeping the others fixed? (which was a suggestion I had but I am unsure how to do it)

If you're using a Gromos96 parameter set, you should start by using the right 
cutoffs:  rlist = rcoulomb = 0.9 and rvdw = 1.4.

Restraining portions of the system to allow other elements to relax is a 
reasonable approach, especially if the failure is occurring so quickly.  If the 
system fails at 700 ps, that indicates some underlying physical instability.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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