[gmx-users] strange bihavior.

Andrey V Golovin golovin at genebee.msu.su
Fri Feb 7 15:18:26 CET 2003

Hello Anton,

Thursday, February 6, 2003, 8:20:43 PM, you wrote:

AF> 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.

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

Yes finally i found mistake.. If some one will use lipid.itp from
Tieleman's site pay attention to line 9 :)) to make random lipid
mixture it's ok but for genbox (water adding) remove that line at all.

Best regards,
Dr. Andrey Golovin                           mailto:golovin at genebee.msu.su
MSU, Moscow, Russia

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