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 ?. Thanks, Bala
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