[gmx-users] Non-zero charged system

David van der Spoel spoel at xray.bmc.uu.se
Wed Mar 27 09:41:40 CET 2002

On Tue, 26 Mar 2002, Tivadar Orban wrote:

>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.

Now the first step is to run grompp again, and use that tpr file for your

>After that mdrun rise the following error:
>   Tolerance         =         1000
>Fatal error: ci = -2147483648 should be in 0 .. 1679 [FILE nsgrid.c, LINE

This is very weird. Can you send me the tpr file that caused this? And
also some information on the machine you are running on.

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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