[gmx-users] Re: how to optimize hydrogen bonds before simulation?

Dr. Vitaly V. Chaban vvchaban at gmail.com
Fri Mar 30 00:14:08 CEST 2012

> Hello:
>   I am wondering is it possible to optimize hydrogen bonds network
> before simulation? I've got some crystal solvent in the system and I
> would like to optimize the hbond network even before building a solvent
> system.

If you freeze all atoms which are not involved in H-bonds, the
coordinates of the remaining atoms will be optimized. Another question
is why you need that "before building a solvent".

Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ. Rochester, Rochester, New York 14627-0216

More information about the gromacs.org_gmx-users mailing list