[gmx-users] Melittin in Methanol.......

[sharada]

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" <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at 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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