[gmx-users] Regarding minimum protein-edge distance and dispersion correction for Charmm27 (Charmm22/CMAP) or Charmm36 FF

[Justin Lemkul]

On 9/28/16 10:28 AM, Rakesh Ramachandran wrote:
> Hi Justin,
>
>      Thanks for the answers. How do I get to know if the box size is
> changing my trajectory or which gmx tool would help me in this ? I have one
> floppy beta sheet insertion in my protein structure and I want to see if it
> has any affect on the box size or periodic images.
>

The box vectors are stored in the .edr file, but the most straightforward way to 
check is gmx mindist -pi, which is designed to check for minimum image violations.

-Justin

> Regards
> Rakesh
>
> On 28 September 2016 at 19:20, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 9/28/16 5:45 AM, Rakesh Ramachandran wrote:
>>
>>> Dear Gromacs users,
>>>
>>>      I am using Charmm36 FF with Gromacs 5.1 GPU version for running my
>>> protein simulations. With respect to the minimum protein-edge distance for
>>> Charmm FF I see in the literature that it should be greater than 1.2nm, as
>>> rcoulomb value is 1.2nm and also for proper screening of electrostatic
>>> interactions between copies of the protein across periodic boundaries.
>>>
>>>     1) My question is can a minimum protein-edge distance of 1.0nm be used
>>> in the protein MD simulations (I see this value in a lot of publications)
>>> and has anyone encountered problems in electrostatic energy values for the
>>> Charmm FF because of using 1.0nm cutoff.
>>>
>>>
>> I would consider a 1.0-nm solute-box distance a bare minimum.  It will
>> satisfy the minimum image convention unless the box size changes
>> drastically.
>>
>>     2) Moreover should dispersion correction be enabled by setting DispCorr
>>> value to Yes for Charmm FF for protein MD simulations.
>>>
>>>
>> http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM
>>
>>     3) Which is the current release which would be ideal to use with Charmm
>>> FF - Gromacs 5.1.4 or Gromacs 2016 ?
>>>
>>>
>> Use of the force field is not version-dependent.
>>
>> -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

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