[gmx-users] Topology file for simulation of inorganic compounds

[Justin Lemkul]

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

-- 
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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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