[gmx-users] About the GROMOS96 parameters files

[Justin A. Lemkul]

intra\sa175950 wrote:
> Dear GMXusers, 
>  
> I would like to reproduce the results obtained in the paper of Marrink et al
> "Molecular dynamics simulations of the kinetics of spontaneous micelle
> formation". J. Phys. Chem. B, 104:12165-12173, 2000". In this (old but
> interesting) work, the authors used the GROMOS96 force field to model the
> DPC lipid. I have found the topology file for the lipid in the P. Tieleman's
> website but not the GROMOS96 lipid parameters. I have contacted one of the
> authors (SJ Marrink), but unfortunately, he has not kept the files.  
> 

The parameters used were not GROMOS96.  See ref. 14 in the paper cited (which 
then leads to ref. 23 of that paper).  There was a custom lipid force field 
developed for those studies.

> Does anyone know where I can find this file in the GROMACS format?
> 

Perhaps one of the original authors of the original reference can help you.

> I have also found a "ffgmx_lipids.tar.gz" file in the "user contribution"
> section of the GROMACS's website. Is this file is the GROMOS96 parameter for
> lipids used in this paper above? 
> 

No.  "ffgmx" refers to the long-since deprecated GROMOS87 force field with other 
ad hoc changes.  See the manual.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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