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 * -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.