[gmx-users] On Decane coordinate file

Bao Kai paeanball at gmail.com
Tue May 21 19:21:41 CEST 2013


Thank you for your response.

I guess I took the problem wrong.  I guess I need a topology file for decane.

I did some google search, generally people told that it can be done
manually, while this is really not my field.  My field is CFD, while
my boss gave me some molecular simulation things to do.

I am wondering if there is some more convenient way to generate the
the decane topology file.

I found some .pdb file, while I failed to generate the .top file with
pdb2gmx. Generally the residue name is not correct.

I wonder if there is anyone have done this before and would like to
provide one .top or .itp file on decane.  Generally any forcefield
will work while OPLS-AA forcefield will be better.

Thank you very much.

Best Regards,
> 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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