[gmx-users] The molecular structure

Justin A. Lemkul jalemkul at vt.edu
Wed Aug 27 00:49:40 CEST 2008

Chih-Ying Lin wrote:
> Hi
> the molecular structure : bond length, bond angle, dihedral angle ....
> the bond length, bond angle are easily determined..
> but the dihedral angle are hard to control...

Are you looking to control (i.e., restrain/constrain) these parameters, or 
measure them?

> with one set of the force field parameter, I could not get the exact
> structure of the molecule (not all of the dihedral  angles are the
> same , but bond length and bond angle are the same)

I should think not!  All bonds are not created equal.  Maybe I'm just missing 
your meaning.  Are you missing a parameter for your molecule?  If so, you'll 
have to derive it, or at least use a comparable parameter.  Are you trying to 
make a measurement?  If so, you haven't provided enough information to get a 
very helpful reply.

> will it affect my rest of simulation severely?

Depends on how you answer the above :)


> Thanks
> Lin
> _______________________________________________
> 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