[gmx-users] Non-zero charged system

Tivadar Orban t.orban at csuohio.edu
Wed Mar 27 12:54:08 CET 2002

On Tue, 26 Mar 2002, Tivadar Orban wrote:

>>I have submitted to the list a problem earlier about the problem that I ha=
>>encountered on my simulation. Erik answered me and I followed his
>>I=B9ll 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=3Dpme inst=
>>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 =B3ions.=
>>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
I thought of that too, after genion I modified the .top file as written
abowe and I tried to run grompp again. This rised up an the following error:

Fatal error: number of coordinates in coordinate file (102Mem.gro, 11462)
             does not match topology (102M.top, 11465)

>>After that mdrun rise the following error:
>>   Tolerance         =3D         1000
>>Fatal error: ci =3D -2147483648 should be in 0 .. 1679 [FILE nsgrid.c, LIN=

>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.
I use Mac G4 with 2 proc. Running under the MacOSX operating system. Has c
compiler, fortran. 
Where should I send you the .tpr file? To gmx-users at gromacs.org or to your
address bellow? It's about 1.6Mb uncompressed, if I compress it it'll be
>Groeten, David.
>Dr. David van der Spoel, =09Biomedical center, Dept. of Biochemistry
>Husargatan 3, Box 576,  =0975123 Uppsala, Sweden
>phone:=0946 18 471 4205=09=09fax: 46 18 511 755
>spoel at xray.bmc.uu.se=09spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel


Tivadar, Orban

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