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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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