[gmx-users] strange bihavior.

[Anton Feenstra]

David van der Spoel wrote:
> On Thu, 2003-02-06 at 13:18, Andrey V Golovin wrote:
> 
>>Hello gmx-users,
>>
>>I did create nice random mixture of lipids, EM was ok Epot=500. But after adding
>>the water (by genbox) EM does not work. Fmax=10e+13 in 50 steps :) very nice one.
>>Probably answer is very simple, if not i'll provide my *.mdp files.
>>
> 
> Could be PBC, a lipid sticking out of the box, while genbox should
> realize this. The high energy seems to say atoms too close to each
> other. I think mdrun tells you which atom it is, so you can kick that
> one out manually.

Or maybe you have generated lipid molecules on top of each other; have
you tried minimizing the lipids before genbox. That is not a necessary
step, but it *will* tell you if the conflict is there already.


-- 
Groetjes,

Anton
  ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
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