[gmx-users] charge groups

[Liu Shiyong]

Hi,

        In the manual:

" Consider a water molecule interacting with another atom. When we would
apply the cutoff an on atom-atom basis we might include the atom-Oxygen
interaction(with a charge of -0.82) without
the compensating charge of the protons and so induce a large dipole moment
over the system. Therefore we have to keep groups of atoms with total charge
0 together. These groups are called charge groups.

So, When I tried to define energy groups  based on chain id
(energy_grps         =  chA chB) , I always get an error.

I don't understand why GROMACS  give an option to define energy groups based
on chain id.

Fatal error:
atoms 4176 and 4182 in charge group 1767 are in different energy groups

PDB:
ATOM   4176  OG  SER A 541     -13.599  44.346  39.228  1.00  0.00      S
1
ATOM   4177  N   ALA A 542     -12.827  48.211  42.079  1.00  0.00      A
1
ATOM   4178  CA  ALA A 542     -12.788  48.960  43.342  1.00  0.00      A
1
ATOM   4179  C   ALA A 542     -12.052  50.279  43.097  1.00  0.00      A
1
ATOM   4180  O   ALA A 542     -12.096  50.830  41.993  1.00  0.00      A
1
ATOM   4181  CB  ALA A 542     -12.084  48.160  44.447  1.00  0.00      A
1
ATOM      1  N   THR B   1      22.984  77.078   8.100  1.00 20.55      T
N



-- 
Shiyong Liu
Postdoc
center for bioinformatics in the university of kansas
Lab: (785)864-1962
Email: syliu at ku.edu (shiyongliu at ku.edu or liushiyong at ku.edu)
Homepage: http://www.people.ku.edu/~syliu
Lab:    http://vakser.bioinformatics.ku.edu/people
Phone:      (785) 864-1962
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