[gmx-users] how to define a pair
Hi, I am performed a all-atom simulation of a membrane-protein system (the starting structure received from CHARMM-GUI server, using charmm36 FF). #include "toppar/charmm36.itp" [ defaults ]; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ1 2 yes 1.0 1.0 I want to add a pair between list of two atoms, say 10-500 (CA atoms). Lets say the distance between them is 0.800 nm. So I define my pairs in the following way, 10 500 1 (4*2.5*0.800**6) (4*2.5*0.800**12) ; where 2.5 is my epsilon. I get some error when I run the simulation (infinite force, exploding simulation). I suspect my definition of C6 and C12 is wrong. Any suggestions would be useful. -manuel -- 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.
[gmx-users] how to define a pair
Hi, I am performed a all-atom simulation of a membrane-protein system (the starting structure received from CHARMM-GUI server, using charmm36 FF). #include "toppar/charmm36.itp" [ defaults ] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 1.0 1.0 I want to add a pair between list of two atoms, say 10-500 (CA atoms). Lets say the distance between them is 0.800 nm. So I define my pairs in the following way, 10 500 1 (4*2.5*0.800**6) (4*2.5*0.800**12) ; where 2.5 is my epsilon. I get some error when I run the simulation (infinite force, exploding simulation). I suspect my definition of C6 and C12 is wrong. Any suggestions would be useful -manuel -- 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.
