[gmx-users] Regarding membrane construction

[Justin Lemkul]

On 6/11/14, 6:25 AM, Venkat Reddy wrote:
> Dear Justin,
> I am following membrane-protein tutorial to construct my system. During
> equilibration and production MD, I am receiving the following NOTES.
>
> NOTE 1 [file md.mdp]:
>    nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
>    nstcomm to nstcalcenergy
>
>
> NOTE 2 [file md.mdp]:
>    leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
>
> I have downloaded the mdp files from tutorial. Is it ok if I omit these
> notes and carry the production run?
>

Notes are just for informative purposes.  Warnings indicate problems.

-Justin

>
> On Tue, Jun 10, 2014 at 5:41 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 6/10/14, 1:12 AM, Venkat Reddy wrote:
>>
>>> I have used
>>> editconf -f protein.gro -c -bt cubic -d 1.5 -o confout.gro
>>> to set the box.
>>>
>>> Then
>>> genbox -cp confout.gro -cs dppc128.gro -o protein_in_membrane.gro
>>> got hanged
>>>
>>>
>>> Am I missing something here???
>>>
>>
>> Don't extend the z-dimension at this stage.  You want to expand the
>> membrane laterally (along x and y, usually), so set the box vectors
>> manually with editconf -box, not -d (though using -d can tell you what
>> suitable vectors in x and y might be).  You can always increase the
>> z-dimension, if you need to, later using editconf and then fill with water
>> using genbox in a separate step.
>>
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> 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 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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