[gmx-users] The simplest em.mdp file for GMX 5 (and perhaps for 4.5)

[Alan]

Thanks Justin,

I forgot to mention but my system is just on small molecule, without
solvent, no box defined in principle. So, basically, I want to see if the
topology is “OK” enough for GMX to not complain, like I used to do, before
doing big things.

Thanks,

Alan

On 27 October 2015 at 12:01, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 10/27/15 7:51 AM, Alan wrote:
>
>> Hi there,
>>
>> I used to have this, just for simple quick test:
>>
>> cat em.mdp
>>
>> integrator               = steep
>> nsteps                   = 500
>>
>> Alas, it does not work anymore with GMX 5.
>>
>>    ERROR: The cut-off length is longer than half the shortest box vector
>> or
>>    longer than the smallest box diagonal element. Increase the box size or
>>    decrease rlist.
>>
>>
>> And my md.mdp (which I didn’t test yet, and I fear it will likely fail
>> too)
>> is:
>>
>> integrator               = md
>> nsteps                   = 1000
>>
>> If I could keep them working for both GMX 5 and 4.5 that would be great.
>>
>>
> The error is related to the size of the system; the default value of rlist
> hasn't changed recently (or ever?) from 1.0 nm, so it seems that your
> bare-bones .mdp file could selectively fail if the system is small or the
> box is incorrectly assigned.  Perhaps it's something related to the Verlet
> scheme becoming the default since 4.5?  The only thing that should affect
> rlist would be verlet-buffer-tolerance.
>
> -Justin
>
> --
> ==================================================
>
> 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
> http://mackerell.umaryland.edu/~jalemkul
>
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-- 
Alan Wilter SOUSA da SILVA, DSc
Senior Bioinformatician, UniProt
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
Tel: +44 (0)1223 494588