[gmx-users] Fwd: using oplsaa in Gromacs

Tsjerk Wassenaar tsjerkw at gmail.com
Sun Mar 15 15:02:37 CET 2009

I refuse to act as a mailing-list subsitute. And there are others
better fit to point you to:



---------- Forwarded message ----------
From: oguz gurbulak <gurbulakoguz at yahoo.com>
Date: Sun, Mar 15, 2009 at 2:50 PM
Subject: using oplsaa in Gromacs
To: tsjerkw at gmail.com

Dear  Dr. Tsjerk,

I study on Molecular Dynamics. I'm planning to do md simulations for
pure and binary mixtures of n-alkane molecules. I use Gromacs 4.0.4. I
want to use oplsaa, but in order to create gro and top files I should
create a .itp file manually or enter a new residue for each n-alkane
molecule into ffoplsaa.rpt file. I also searched about this to learn
much about these procedures. I saw your mails in mail archive and
though that you can lead me to do the right thing. I want to ask you
which is the true and easy way :

1.      To create a .itp file manually residue for each n-alkane

2.      To enter a new residue for each n-alkane molecule into ffoplsaa.rpt

Could you please give me the information about these procedures ? I
would be very grateful if you can help me to choose the right way.
Also, Can I use ffG43a2 force field for n-alkane md simulations ?

Thank you very much for your attention.



Ege University - Faculty of Science

Department of Physics

e-mail: oguzgurbulak at mail.ege.edu.tr

Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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