On 8/13/12 1:49 PM, Deepak Ojha wrote:
Dear All
I want to do simulation of some ions like azide ion,thiocynate ion and
other inorganic compounds in liquid water.
I am not sure how to generate topology file for the same.How can I go
about doing the same.
Likely you will have to do it manually, which means you will have to understand
Chapter 5 of the manual and the proper parameterization protocol for your
molecules under the chosen force field.
Some web servers exist for such purposes, depending on the force field you want
to use. Otherwise consult the following page and be prepared for a significant
time investment:
http://www.gromacs.org/Documentation/How-tos/Parameterization
-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@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Only plain text messages are allowed!
* 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-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
