[gmx-users] Non-zero charged system

Tivadar Orban t.orban at csuohio.edu
Wed Mar 27 02:04:30 CET 2002

I have submitted to the list a problem earlier about the problem that I have
encountered on my simulation. Erik answered me and I followed his
I¹ll make a short description of the problem:
After preparing the system, at energy minimization grompp informed me that
the system has a non-zero charge (+1). I want to use rculomtype=pme instead
of cut-off, so I ran genion with 1 Cl ion, I think that it will not give
born to considerable artifacts.
After genion I manually modified the .top file by adding #include ³ions.itp²
and at the end after [System] adding the Cl 1.

After that mdrun rise the following error:

   Tolerance         =         1000
Fatal error: ci = -2147483648 should be in 0 .. 1679 [FILE nsgrid.c, LINE

This is the first problem.
The second one is regarding the .tpr file.
In order to perform mdrun with an uncharged system, should I modify somehow
the .tpr file, the input for mdrun.
Because I think that I ca not use the same .tpr for mdrun that I have used
to uncharge the system with genion.

Tivadar, Orban  

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