[gmx-users] No domain decomposition

Justin Lemkul jalemkul at vt.edu
Mon Sep 28 14:55:07 CEST 2015

On 9/28/15 8:49 AM, Chandan Choudhury wrote:
> g_tune_pme would give some useful information.
> On Mon, Sep 28, 2015 at 6:05 PM, soumadwip ghosh <soumadwipghosh at gmail.com>
> wrote:
>> Hi Chandan,
>>                   I tried it once using -nt option but it failed . I
>> kept it 8 although I dont know how to change the number of nodes for
>> mdrun correctly. How do I know the value of x if I want to run say
>> mdun -deffnm mdfinal -nt x. It is worth mentioning here that for my
>> NPT and NVT mdrun proceeded smoothly and I am being troubled only in
>> the production run stage. i would appreciate any sort of help. One
>> more question - from the crashed mdfinal.log file is it possible to
>> have some information about domain decomposition or the approximate
>> value of -nt x?

The DD failure is symptomatic of unstable physics, not causative of it. 
Regardless of how many threads/cores you use, an unstable system will always 
crash.  You need to have a thorough look through 



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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