[gmx-users] how to write .top file for a rigid molecule

Justin A. Lemkul jalemkul at vt.edu
Wed Nov 12 04:31:51 CET 2008

Jinyao Wang wrote:
> gmx-users,
> I am goning to carry out a rigid system system simulation for Benzaldehyde. Atom charges,Bonds and Angles come from Gaussion03 computation.  LJ interaction parameters come from oplsaa forcefield. I don't know how to deal with rigid molecules in gromacs. So I couldnot know how to write the .top file for the rigid Benzaldehyde. If you could give me some suggest, It is appreciated.

Do you define "rigid" as "containing constrained bonds"?  You should be able to 
choose appropriate bonded parameters from ffoplsaabon.itp, but in the .top all 
you would have to specify are the atom numbers involved in the bond; as long as 
there are parameters for that particular bond, they will be read from 


>         Jinyao Wang
>         wangjy at ciac.jl.cn
>           2008-11-12
> ------------------------------------------------------------------------
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list