[gmx-users] Basic GROMACS questions

[Justin Lemkul]

On 12/8/14 4:47 AM, Simone Bolognini wrote:
> Hi!
> I started using GROMACS like 2-3 weeks ago and I'm doing the first steps in
> the comprehension of the subject (I'm a physicist, but not skilled in
> molecular dynamics). Therefore, I have some basic questions to ask to you:
> 1) are there any conceptual problems in using different running parameters
> for "in solvent" energy minimization, position restrained dynamics and
> dynamics? For example: would it lead to some "absurd results" if I use
> Berendsen pressure and temperature coupling for position restrained
> dynamics and Nose-Hoover and Parrinello-Rahman for the actual dynamics?

This is a rather typical protocol.  The weak coupling algorithms are very 
forgiving and converge quickly, so they are useful for equilibration.

> 2) which is the most reliable force field for GROMACS 4.5.6? For all my
> simulations I always used the last version of the Gromos ones: would you
> suggest something different?

There is no answer to this question.  The "most reliable" depends on the system 
being considered and which force field(s) has(have) been shown to adequately 
model the dynamics of interest.

> 3) for the dynamics of a protein, would you use PME electrostatics or
> Reaction-Field one? Again: is there any conceptual problem in using
> different electrostatics parameters in the different stages of simulation?
> I would guess there are, but in the various tutorials I saw it seems that
> many people change settings "on the run".

Haphazard changes are inadvisable.  PME is generally considered the "best" 
method for most, if not all, modern force fields, but of course, as with all 
things in science there are caveats and not universal agreement.  PME is, 
undoubtedly, the most widely used method.

> 4) in a perfect world, where running time is not a problem, what kind of
> .mdp file would you set for the dynamics of a small protein? I mean: is
> there a general recipe to do things correctly (and in a realistic fashion)
> or is it really case dependent?
>

Nonbonded settings depend on the force field being used.  Most other settings 
are fairly boilerplate, but if you want specific commentary, you need to provide 
an actual .mdp - too many possible settings to be guessed at :)

-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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