sharada wrote:
Thanks for the reply.
I am sorry about the typo mistake, it is 45a3 forcefield that I am
working with & that I choose by giving the option 3 in pdb2gmx. So with
PME the epsilon_r value has to be mentioned ?.Are the different
forcefields 43a1,45a3 etc have to be used with different sets of rvdw,
rcoulomb & rlist ? In that case what would be the set of values if I am
working with 45a3 forcefield with PME option ? How do I give correction
term for dispersion otherwise? Are the methanol .gro and itp files that
I am taking the right ones ?
Most of these questions can be answered by taking my earlier advice and reading
the literature reference for the derivation of the force field. You should not
blindly choose a force field without understanding how it was derived and what
it is used for, as well as how to use it. There is no substitute for doing your
homework.
As an aside, the 53a6 parameter set (as I suggested before) represents an
improvement upon the 45a3 parameters; you may consider using it instead since it
is newer and more accurate (within the criteria chosen by the developers of the
force field). Again, more reading will help you make in informed choice.
I see no reason to specify epsilon_r as anything other than the default (don't
confuse it with epsilon_rf, either). As for dispersion correction, read about
the .mdp option DispCorr.
The methanol.gro and .itp files may or may not be what you want. Typically the
Gromos96 derivations are done with amino acid analogs (side chains), so the
parameters for methanol are likely the same as for the serine side chain.
Again, read the primary literature, and do not blindly use a topology you think
might be appropriate. Probably with correct parameters, the .gro file will
suffice, provided you use an adequate equilibration scheme.
-Justin
regards,
sharada
*/-- Original Message --/*
From: "Justin A. Lemkul" <jalem...@vt.edu>
To: "Gromacs Users' List" <gmx-users@gromacs.org>
Date: Sat, 31 Jan 2009 07:35:42 -0500
Subject: Re: [gmx-users] Melittin in methanol...
sharada wrote:
> Hello Justin,
>
> Thanks for the reply . I apologise for the repeat mail. The parameters
> are for ffG43a3 forcefield. Yes I am using the default electrotatics
> cutoff values as an initial run. I would change to PME method as you
> say. However I was wondering If r_epsilon value equals to 66 contributes
> to a change in the simulation or this value holds good only if reaction
> field is on ?
>
I have never heard of 43a3, do you mean 43a1, or perhaps 45a3? Better be
sure
about what you're using so you get the .mdp options right. Use PME, and
make
sure your values of rlist, rcoulomb, and rvdw are for use with that
particular
parameter set (rvdw = 0.8 is particularly troubling, especially in the
absence
of any dispersion correction).
With cut-off, the epsilon_r parameter is probably meaningless.
-Justin
> sharada
>
>
> */-- Original Message --/*
> From: "Justin A. Lemkul" <jalem...@vt.edu>
> To: Discussion list for GROMACS users <gmx-users@gromacs.org>
> Date: Sat, 31 Jan 2009 00:42:36 -0500
> Subject: Re: [gmx-users] Melittin in methanol...
>
>
>
> sharada wrote:
>
> > rlist = 0.5
> > rcoulomb = 1.4
> > rvdw = 0.8
>
> You are using cut-off electrostatics by default, so you are probably
> getting
> some bad artifacts (use PME instead). Also, the values of rlist,
> rcoulomb, and
> rvdw you are using do not correspond to those for which the Gromos96
> force field
> was derived. These make no sense. Refer to the original literature for
> whichever parameter set you decided to use.
>
> -Justin
>
>
> --
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> _______________________________________________
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
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Please search the archive at http://www.gromacs.org/search before posting!
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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