[gmx-users] Melittin in methanol...

[Justin A. Lemkul]

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" <jalemkul at vt.edu>
> To: "Gromacs Users' List" <gmx-users at 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" <jalemkul at vt.edu>
>  > To: Discussion list for GROMACS users <gmx-users at 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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-- 
========================================

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

========================================