[gmx-users] Fwd: Help with Gromacs 5.1 mdp options for CHARMM27 force field

[Rakesh Ramachandran]

Hi Justin,

   Thanks for the reply. Why is the RMSD difference reported by gmx energy
tool so large after NPT equilibration as well as energy minimization ? I
did not find such difference in RMSD when I superimposed the structures
onto the crystal structure.

*Energy Min*

Energy                      Average   Err.Est.       RMSD  Tot-Drift
-------------------------------------------------------------------------------
Potential                -1.27808e+06      45000     120456    -293146
 (kJ/mol)

*NPT equil*

Energy                      Average   Err.Est.       RMSD  Tot-Drift
-------------------------------------------------------------------------------
Pressure                  -0.905575        1.8    99.0051    9.72043  (bar)

Regards
Rakesh


On 11 December 2015 at 19:41, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 12/11/15 8:49 AM, Rakesh Ramachandran wrote:
>
>> Hi Justin,
>>
>>       Thanks for the reply. Are nstlist and rlist options important for
>> GPU
>> based gromacs and Verlet cutoff ? I am using nstlist value of 40 and rlist
>> of 1.2 are these appropriate for CHARMM36.
>>
>>
> Verlet tunes both of these as needed.  rlist is automatically adjusted to
> never miss interactions.  The input value is a minimum value; mdrun takes
> care of the rest.
>
> Moreover why is force-switch a better option than other vdw-modifier
>> options for CHARMM36 ?
>>
>>
> This is the method with which the force field was parametrized.  It is
> absolutely required for membrane systems.  Proteins and nucleic acids can
> be debated, but unless you have a rock-solid, verified, reason to change
> the vdW method, don't.
>
>
> -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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