[gmx-users] On Decane coordinate file

[Justin Lemkul]

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

-- 
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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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