[gmx-users] On Decane coordinate file

Justin Lemkul jalemkul at vt.edu
Tue Apr 16 14:40:56 CEST 2013

On 4/16/13 6:51 AM, Bao Kai wrote:
> Dear all,
> I am trying to do some two phase simulations with Decane molecules and some
> other smaller molecules.
> When I did simulations with smaller molecules, I specifies the properties
> based on each atom, while I just realized it is really not desirable to do
> it with Decane molecules ( 34 atoms each molecule).
> I am wondering if anyone could provide one coordinate file and the itp ( or
> .top ) file for the Decane simulation if you have ever done it before.  I
> did not find very detailed Decane molecule models.

You should probably mention what force field you're trying to work with.  For a 
simple alkane like decane, writing the necessary .rtp and .hdb (if necessary) 
entries is fairly trivial.  Then just let pdb2gmx do all the work assembling the 
whole topology.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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