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

[Rakesh Ramachandran]

Hi Justin,

   Thanks for the answer.

Regards
Rakesh

On 28 September 2016 at 20:00, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> ==================================================
> --
> Gromacs Users mailing list
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