[gmx-users] Bug with system total charge?
DimitryASuplatov
genesup at gmail.com
Wed Feb 25 20:27:51 CET 2009
Hello,
I am running a simulation of a protein in 10M urea (Smith topology) and spce water.
I run energy minimization in vacuum, then use genbox to add mixed solvent, then run grompp and receive the following message:
System has non-zero total charge: -8.999696e+00
Then I use genion to add 80 NA+ and 71 CL- (I use opls) in exchange on SOL molecules. Resulting top file looks like this
===========================================
#define HEAVY_H
; Include forcefield parameters
#include "ffoplsaa.itp"
; Include chain topologies
#include "1klc.5toA.300.urea.spce_A.itp"
#include "1klc.5toA.300.urea.spce_B.itp"
; Include water topology
#include "urea.smith.itp"
#include "spce.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include generic topology for ions
#include "ions.itp"
[ system ]
; Name
Protein in water
[ molecules ]
; Compound #mols
Protein_A 1
Protein_B 1
UREA 5130
SOL 15796
NA+ 80
CL- 71
=======================================================
Everything seems fine but when I run grompp again to start energy minimization in solvent I receive a devastating comment:
System has non-zero total charge: 3.043525e-04
!!!
No complaints about incompatibility between top and gro. The order of groups in top and in gro are synchronized (PROTEIN, UREA, SOL, NA+, CL-).
I tried to add only 1 NA+ and this changed the result to: System has non-zero total charge: -7.999696e+00
2NA+: System has non-zero total charge: -6.999696e+00
1NA+ and 1CL- : System has non-zero total charge: -8.999696e+00
71NA+ and 71CL-: System has non-zero total charge: -8.999696e+00
73NA+ and 71CL-: System has non-zero total charge: -6.999696e+00
75NA+ and 71CL-: System has non-zero total charge: -4.999696e+00
77NA+ and 71CL-: System has non-zero total charge: -2.999696e+00
78NA+ and 71CL-: System has non-zero total charge: -1.999696e+00
79NA+ and 71CL-: System has non-zero total charge: -9.996956e-01 !!!!!!!!!!!!!!!
and finally
80NA+ and 71CL-: System has non-zero total charge: 3.043525e-04 !!!!!!!!
Number of ions included by genion is always appropriate. Number of UREA atoms always stays the same. I tried gromacs 4.0.4 and 4.0.2 - same result!
Never had that problem before. Must be some issue with urea topology but I can not figure it out myself. Any suggestions?
Thanks.
SDA
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