[gmx-users] On Decane coordinate file

[Naga Rajesh Tummala]

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