[gmx-users] genion

Pedro Alexandre de Araujo Gomes Lapido Loureiro paloureiro at biof.ufrj.br
Fri Mar 8 17:31:30 CET 2002

Dear GROMACS users/developers,

after using the program genion, to insert a Cl ion a box containing a peptide 
in water I got the following warnings/errors:

1)After runnig the program grompp (mshion.top and mshion1-1.gro already contain 
the ion):

"Warning: atom names in mshion.top and mshion1-1.gro don't match (Cl - OW)
(more than 20 non-matching atom names)
Warning 7 [file "mshion.top", line 33]:
  33145 non-matching atom names
  atom names from mshion.top will be used
  atom names from mshion1-1.gro will be ingnored"

In the .top file I had already added one Cl atom and deleted one water molecule.
Am I doing somethig wrong?

2)When using the random insertion mode in the genion, later when I run a 
conjugate gradient minimization (after having runned a steepest descent without 

"Conjugate gradients:
   Tolerance         =  1.00000e+02
   Starting Energy   = 1.639584000000000e+09
   F-Norm            =  6.35435e+07

Step 1, E-Pot = 1.6376719360e+09, F-max =  5.34807e+10
Fatal error: ci = -2147483648 should be in 0 .. 2495 [FILE nsgrid.c, LINE 214]"

What does it mean ?
There was an e-mail with this kind of error in the list, but I was not able to 
find any reply.

3)Using the electrostatic insertion mode gives the same error, when I use mdrun 
to run a conjugate gradient minimization

Thank you for any suggestion.
Pedro Alexandre Lapido Loureiro
Laboratório de Física Biológica
Instituto de Biofísica

More information about the gromacs.org_gmx-users mailing list