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
--
========================================
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
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
