[gmx-users] Re: grompp for minimization: note & warning

shahab shariati shahab.shariati at gmail.com
Mon Sep 16 16:52:23 CEST 2013

Dear Justin

Very very thanks for your quick reply.

> The sys.gro file is positioned within a box that is too large, a fact that is
> easily observable in VMD.  I suspect that the void space results in instability.

If I positioned system in a smaller box, my problem  (instability) solved ???

> As for the charge group error from grompp, I still can see no reason for it.

In the first e-mail, I put charge groups, as you seen, they were ok and true.

Thus what is reason of charge group error from grompp.

Please guide me to resolve these issues.

Best wishes

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