On 5/21/13 1:44 PM, Bao Kai wrote:
Hi, Rejesh,
Thanks for the reply.
Unfortunately, they does not have the topology file for decane.
For a simple molecule like decane, g_x2top can probably create a reasonable
topology for you.
-Justin
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
========================================
------------------------------
--
gmx-users mailing list
gmx-users at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
End of gmx-users Digest, Vol 108, Issue 106
*******************************************
--
gmx-users mailing list gmx-users at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
========================================
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
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
