[gmx-users] md simulation of oil hydrocarbon / L-OPLS

Smith, Micholas D. smithmd at ornl.gov
Tue May 29 21:14:04 CEST 2018

Since octane is not huge hydrocarbon, you could use LigParGen ( http://zarbi.chem.yale.edu/ligpargen/gmx_tutorial.html ) from Jorgensen's lab to generate an itp file for octane, which you could use as your guide to build an rtp.


Micholas Dean Smith, PhD. MRSC
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics

From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin Lemkul <jalemkul at vt.edu>
Sent: Tuesday, May 29, 2018 3:10 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] md simulation of oil hydrocarbon / L-OPLS

On 5/29/18 3:08 PM, Atila Petrosian wrote:
> I know your mean. But there is not octane residue type in rtp file.

Then you'll have to make one, using the existing molecules as a guide.
The OPLS atom types for such a species should be straightforward to assign.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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