[gmx-users] total charge of the system

[ahmet yıldırım]

Hi,

In my simulation, total charge of the system is a noninteger number (System
has non-zero total charge: 8.000004e+00). I neutralized it with 8 chlorine
atoms.
Then, grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr

Fatal error:
moleculetype CU1 is redefined
is it some thing wrong?

Below is the first and final version of the .top file:

First topol.top File
*....*
[ molecules ]
; Compound        #mols
Protein_chain_P     1
Protein_chain_L      1
Protein_chain_H     1
SOL                     10
SOL                    127
SOL                    157
SOL                 41779
**

Final topol.top File
*#include "ions.itp"*

[ molecules ]
; Compound        #mols
Protein_chain_P     1
Protein_chain_L      1
Protein_chain_H     1
SOL                     10
SOL                    127
SOL                    157
SOL                 *41771*
*CL-                         8*






-- 
Ahmet YILDIRIM
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