[gmx-users] Gromacs

David van der Spoel spoel at xray.bmc.uu.se
Thu Jan 12 14:25:55 CET 2017

On 12/01/17 10:11, Dilip H N wrote:
> i have a molecule of an acid...
> how can i create a topology file from that and do the simulation..??
> i cant use gmx pdb2gmx -f file.pbd -o file.gro ....
> since it asks force feild , and thn water model..??
> i dont want water to be added (since it is asking water model)...
> how can i proceed with my acid molecule for simulation..??
> Thank you...
What acid?

Maybe you should rad chapter 5 of the manual, run a few tutorials and 
then head over to http://virtualchemistry.org

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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