[gmx-users] SMD - Pulling Error in mdrun 0.49 times box size

Justin Lemkul jalemkul at vt.edu
Wed Nov 26 04:30:34 CET 2014

On 11/25/14 6:35 PM, Agnivo Gosai wrote:
> Mr. Law
> I understand your argument regarding the box length along the Z axis but
> for the same box length I did complete 2 successful SMD runs of 500 ps and
> 1 ns , having different pull rates but in effect the same pulled distance
> of 5 nm. Only in the 5 ns SMD , the mdrun crashed with the error as
> mentioned in my initial ( trailing ) mail.

Different pull rates of the spring mean the dynamics of the system are 
different.  Just because two systems "worked" doesn't mean any other necessarily 
will.  You're living dangerously by trying to pull exactly half the box when 
using pressure coupling.

> My question is , why I need to change box dimension now ? Or may be because
> I am simulating under an NPT ensemble , the box vectors had enough time to
> change and thus contribute towards the error ?

You probably got lucky twice and now you're not lucky.  It's a simple thing to 
plan for - pad the box a bit with NPT.  Or use a pull-geometry that is not 
sensitive to periodicity (like direction-periodic).



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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