Dear Gromacs community,
I am using Gromacs to simulate a C-alpha structure and have the following
topology file (created by http://smog-server.org/).
[ defaults ]
;nbfunc comb-rule gen-pairs
1 1 no
[ atomtypes ]
;name mass charge ptype c10 c12
CA 1.000 0.000 A 0.000 0.167772160E-04
[ moleculetype ]
;name nrexcl
Macromolecule 3
[ atoms ]
;nr type resnr residue atom cgnr charge mass
1 CA 1 ASN CA 1 0.000 1.000
2 CA 2 LEU CA 2 0.000 1.000
3 CA 3 LYS CA 3 0.000 1.000
4 CA 4 THR CA 4 0.000 1.000
....
[ pairs ]
; i j type and weights
2 25 1 0.198921701E+01 0.132925132E+01
2 27 1 0.582768432E+02 0.765215442E+02
2 45 1 0.865830453E+01 0.776440056E+01
3 7 1 0.143745898E+02 0.142660275E+02
3 8 1 0.458838723E+02 0.574355228E+02
...
As I understand, VDW parameter will only be generated by grompp for pairs
of atoms which are defined in the directive [pairs]. When I use grompp, the
notification is:
Generated 1 of the 1 non-bonded parameter combinations.
Based on the above topology ([pairs]) i expected there are more non-bonded
combination generated. Can anyone help me to explain this?
Also:
[ atomtypes ]
;name mass charge ptype c10 c12
CA 1.000 0.000 A 0.000 0.167772160E-04
At first, I thought it meant that the pairs which were not defined in the
directive [pairs] will be repulsive only, but they choose genpairs=no, so
it looks like there is nothing to do with the lines??
Please help me! Thanks in advance.
Best regards,
*Lan Hoa *
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