[gmx-users] charged group problem

[Adriana Garro]

Dear users,

My system contains peptide + TFE + water in an octahedron box.
I am using oplsaa.ff
I am trying to do EM but running this command

grompp -f em.mdp -c  C22_TFE-W.gro -p topol.top -o em.tpr

the next error message come up

WARNING 1 [file em.mdp]:
  The sum of the two largest charge group radii (2.045171) is larger than
  rlist (1.000000)

I am afraid of changing the em.mdp parameters because as I understand these
are the correct for my force field.
I'd really appreciate suggestions!
Thanks in advance


Adriana


here a part of the em.mdp file

nstlist        = 1
ns_type        = grid
rlist          = 1.0
coulombtype    = PME                        ; Use particle-mesh ewald
rcoulomb       = 1.0
rvdw           = 1.0

I read that large charge groups indicate that a fair number of atoms have
been included in the same charge group. Usually only two or three atoms are
in a charge group, rendering them fairly small.

Looking in the TFE.itp, it's true, the whole molecule is in the same
charged group

     1   opls_160      1    TFE   CA3F      1      0.126     12.011   ;
qtot 0.126
     2   opls_161      1    TFE   CF3F      1      0.532     12.011   ;
qtot 0.658
     3   opls_162      1    TFE   OH3F      1     -0.635    15.9994   ;
qtot 0.023
     4   opls_163      1    TFE   HO3F      1      0.429      1.008   ;
qtot 0.452
     5   opls_164      1    TFE   F13F      1     -0.206    18.9984   ;
qtot 0.246
     6   opls_164      1    TFE   F23F      1     -0.206    18.9984   ;
qtot 0.04
     7   opls_164      1    TFE   F33F      1     -0.206    18.9984   ;
qtot -0.166
     8   opls_165      1    TFE   H13F      1      0.083      1.008   ;
qtot -0.083
     9   opls_165      1    TFE   H23F      1      0.083      1.008   ;
qtot 0


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Dra. Adriana D. Garro
Química Medicinal
Facultad de Química, Bioquímica y Farmacia
Universidad Nacional de San Luis
IMASL-CONICET
San Luis, Argentina

Tel..............:+54 266 4424689  int 6153
e-mail...: adgarro at unsl.edu.ar
e-mail...:  adrianagarrosl at gmail.com


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