[gmx-users] doubts on gen-pairs

Bala subramanian bala.biophysics at gmail.com
Mon May 14 11:55:03 CEST 2012

Dear gmx-users, I have some doubts on the manual pages. Kindly help to
understand the same.

Section 5.7.1 Page 129

1) gen-pairs: Setting ‘yes’ generates 1-4 parameters that are not present
in the pair list from normal Lennard-Jones parameters using fudgeLJ.

Is there any way that I can see/write the generated parameters in a file.

Section 5.7.1 Page 130

2) Note that gen-pairs, fudgeLJ, fudgeQQ, and N are optional. fudgeLJ is
only used when generate pairs is set to ‘yes’, and fudgeQQ is always used.

Does it mean that if i specify gen-pairs as "no" and give the pair
parameters explicitly in the topology file, scaling of LJ would be ignored.
I simply want to check the consistency in the energies using gen-pair:yes
and gen-pair:no (giving the parameters explicitly).

3) Section 5.7.1 Page 130

[ dihedrals ] : …. If you want to include Ryckaert-Bellemans type dihedrals
in a topology, do the following (in case of e.g. decane):

[ dihedrals ]

; ai aj ak al funct c0 c1 c2

1 2 3 4 3

2 3 4 5 3

and do not forget to erase the 1-4 interaction in [ pairs ]!

Someone please help me to understand why the 1-4 interaction should be
omitted for RB type dihedrals ?.
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