[gmx-users] On Decane coordinate file

[Bao Kai]

Hi, Rejesh,

Thanks for the reply.

Unfortunately, they does not have the topology file for decane.

Best Regards,
Kai


virtualchemistry.org has some topology files for many organic liquids.


Regards
Rajesh

On Tue, May 21, 2013 at 1:21 PM, Bao Kai <paeanball at gmail.com> wrote:

> Hi,
>
> 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,
> Kai
> >
> >
> > 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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-- 
Naga Rajesh Tummala, PhD
Post-Doctoral Researcher,
School of Chemistry and Biochemistry,
Georgia Institute of Technology