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: [email protected] ([email protected] or [email protected])
Homepage: http://www.people.ku.edu/~syliu
Lab: http://vakser.bioinformatics.ku.edu/people
Phone: (785) 864-1962
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