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

[Justin Lemkul]

On 12/9/15 12:42 PM, Rakesh Ramachandran wrote:
> Hi Justin,
>
>       Thanks for the reply. Sorry if this question was too long or I was not
> clear.
>
> 1) What are the optimal values of tau_t and tau_p for CHARMM36. I see
> in your tutorial that it is 0.1 0.1 for tau_t and 2.0 for tau_p.
> The CHARMM-GUI generated mdp settings had 1.0 1.0 for tau_t and 5.0 for
> tau_p. So are higher values more appropriate for CHARMM36 FF and what
> properties does it effect ?
>

Again, to be absolutely clear, values of tau_t and tau_p are in no way connected 
with specific force fields.

The values affect barostat response times and the distributions of temperature 
and pressure values. Too short and the simulations can become unstable, too long 
and the subsequent values may drift a bit before being restored. Sometimes 
longer times are necessary for heterogeneous systems like membranes. These are 
things you must decide based on whatever your system is and whatever you find in 
the literature. I am not going to tell you what values you should use.

> 3) I was asking Berendsen pressure coupling with respect to the
> equilibration stage, since I read in some earlier mailing post that
> Berendsen coupling is more appropriate for temperature (NVT) as well as
> pressure (NPT) equilibration.
>

Yes, for equilibration, Berendsen is often better because it relaxes quickly.

> 4) Moreover once I do pbc correction I still see one or two ions sticking
> out of the rhombic dodecahedron box representation in pymol. Is it more of
> a visualization artifact ?
>

Yes, just a visualization artifact.

-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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