Hi,
Thankyou for the prompt response. I am using the methanol box provided along
with gromacs software
This is the itp file I am using ...
usr/local/gromacs/share/gromacs/top$ more methanol.itp
#ifndef _FF_GROMOS96
[ atomtypes ]
; type mass charge ptype c6 c12
OMET 15.999 -0.69 A 2.6169e-3 2.5231e-6
OW 15.999 -0.82 A 2.6170e-3 2.6330e-6
CMET 15.035 0.29 A 8.8758e-3 17.8426e-6
H 1.008 0.4 A 0.0 0.0
HW 1.008 0.41 A 0.0 0.0
#endif
[ moleculetype ]
; name nrexcl
Methanol 2
[ atoms ]
; nr type resnr residu atom cgnr charge mass
#ifdef _FF_GROMOS96
1 CMET 1 MeOH Me1 1 0.176 15.035
2 OMET 1 MeOH O2 1 -0.574 15.999
3 H 1 MeOH H3 1 0.398 1.008
#else
1 CMET 1 MeOH Me1 1 0.29 15.035
2 OMET 1 MeOH O2 1 -0.69 15.999
3 H 1 MeOH H3 1 0.40 1.008
#endif
[ bonds ]
; ai aj funct c0 c1
1 2 1 0.13600 376560.
2 3 1 0.10000 313800.
[ angles ]
; ai aj ak funct c0 c1
1 2 3 1 108.53 397.5
I would try using the new force field.
sharada
-- Original Message --
From: "Justin A. Lemkul" <jalem...@vt.edu>
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Date: Thu, 29 Jan 2009 08:47:34 -0500
Subject: Re: [gmx-users] Melittin in Methanol.......
sharada wrote:
> Hello,
>
> I am doing a simulation of melittin molecule in methanol box for 3 ns.
> I am finding that it is unfolding very rapidly and is behaving more like
> in water.
> Melittin behaviour in water, methanol and also in lipids is well
> documented and known since quite some time. I am using the
> methanol216.gro provided along with gromacs software. I am using ffG43a3
> force field. The density of methanol is around 771.238 g/l. The
> backbone rmsd shoots up to 0.5nm immediatly after 500 ps which
> indicates that it is unfolding. I have no clue why it is behaving in
> this manner. Melittin unfolds in water like this but not in methanol.
> Can any one tell me where I am going wrong. Any insight in this
> direction is welcome.
>
Several possibilities. What parameters are you using for methanol? Did you
derive them yourself, or did you obtain them from somewhere else?
Also, you can consider using a newer (improved) force field, like Gromos96 53a6.
-Justin
> Thankyou in advance
>
> sharada
>
>
>
>
> ------------------------------------------------------------------------
>
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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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