[gmx-users] Non-zero charged system

Alan Wilter Sousa da Silva alan at biof.ufrj.br
Wed Mar 27 15:00:05 CET 2002


	I cannot know much about MD but I really think that you'd better
use simple cut-off with Reaction Field. Just one (+1) charge!  I believe
that counter-ions (and thus PME or similar) will give more problems than

On Tue, 26 Mar 2002, Tivadar Orban wrote:

> Hi,
> 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
> directions.
> 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
> 214]
> 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.
> Regards,
> Tivadar, Orban
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Alan Wilter S. da Silva
 Laboratório de Física Biológica
  Instituto de Biofísica Carlos Chagas Filho
   Universidade do Brasil/UFRJ
    Rio de Janeiro, Brasil

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