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

[Rakesh Ramachandran]

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.

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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