[gmx-users] Cyclohexane as a solvent

Justin Lemkul jalemkul at vt.edu
Thu Jul 11 19:14:11 CEST 2013

On 7/11/13 8:59 AM, Shima Arasteh wrote:
> Dear all,
> I see cyclohexane parameters in top & par CGenFF files. Would it be correct if I add this molecule to the rtp file in charmm and then use it as a solvent rather than for example water?

The .rtp mechanism is generally used for building blocks of larger molecules, 
for which topologies are built with pdb2gmx.  There's nothing wrong with 
building an .rtp, but it's probably about the same work as building an .itp, and 
then you have to run pdb2gmx and modify the topology it gives you (from .top to 
.itp).  Save some work and just write the .itp file, especially since you 
already have all the parameters.

> Generally, how is it possible to add a new solvent to the charmm ff simulations?

Like you would any other standalone molecule - write an .itp for it.



Justin A. Lemkul, Ph.D.
Postdoctoral Associate

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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