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

[Justin Lemkul]

On 10/27/15 8:13 AM, Alan wrote:
> 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.
>

I'm not sure how such a setup would have ever worked with those .mdp files.  If 
the box is undefined (e.g. all components are zero), then the default .mdp 
options would have always complained unless you have set pbc = no.

So the workaround is to define a box, turn PBC off, or set cutoffs to zero. 
This would also be backwards compatible with 4.5.

-Justin

> 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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>
>
>

-- 
==================================================

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

==================================================