[gmx-users] Problems with ion names in OPLS and gromacs 4.0.2

[DimitryASuplatov]

Hello,
thanks for the tip about -pname flag for genion - that was the problem in the first place.

While I was waiting for the reply I set -maxwarn=1 and ran the simulation. At the end I got the gro file with the following lines

. . . .
31598SOL     OW 5239   7.367  10.098   9.759 -0.9983 -0.8372 -0.3184
31598SOL    HW1 5240   7.442  10.103   9.693 -0.1595 -1.8795  0.4694
31598SOL    HW2 5241   7.280  10.115   9.713 -0.2726  1.4897 -1.0786
31599NA+     NA 5242   9.240   1.342   5.490  0.0506  0.7314  0.4913
31600NA+     NA 5243   1.452   0.891   5.672  0.0663 -0.3132 -0.0275
31601NA+     NA 5244   0.332   0.852  10.563 -0.4915 -0.6099  0.0614
. . . .
31679CL-     CL 5322   1.332   0.993  10.254 -0.1729 -0.0048 -0.2991
31680CL-     CL 5323   0.142   3.208   2.770  0.2592  0.3646  0.0936
31681CL-     CL 5324   0.681   2.561   5.594 -0.0556  0.0660  0.1265
31682CL-     CL 5325   0.112   3.607   8.225  0.1200 -0.0190  0.0017
. . . .

I guess this names are OK - grompp has taken them from top file to replace old gro names.

SDA