[gmx-users] Re: Segmentation fault 4
feenstra at chem.vu.nl
Fri Apr 4 15:35:01 CEST 2003
Tanos C. C. França wrote:
> Dear Anton
> I am trying a minimization of my cofactors in Gaussian but it's
> not working well. Anyway I will continue trying.
I meant a minimization in Gromacs, using mdrun. That will tell you if
the energy minimum described by the topology and forcefield you are
using (for the MD), is actually reasonable.
> I used genion to add Na+ atoms. 12 molecules of water were
> replaced by the Na+ molecules. I did a visual inspection of the system
> with ngmx, after minimization with steep and cg, and saw that the Na+
> atoms were quite dispersed in the system. Most of them were in the
> solvent and some were inside the protein structure.
I'm not certain they should en up *inside* the protein. Be sure to check
the direct environemt of the Na+ in the protein for possible distortion.
P.S. I really want to keep these discussions on the gmx-users list. That way
others can also learn from my replies, and your questions, but also others
(possibly more knowledgable) can answer you.
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 |
| | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/ |
| | "If You See Me Getting High, Knock Me Down" |
| | (Red Hot Chili Peppers) |
More information about the gromacs.org_gmx-users