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

[Rakesh Ramachandran]

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.

Moreover why is force-switch a better option than other vdw-modifier
options for CHARMM36 ?

Regards
Rakesh

On 9 December 2015 at 23:27, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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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