[gmx-users] Re: Segmentation fault 4

[Anton Feenstra]

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.


-- 
Groetjes,

Anton
   _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| 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)                               |
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