Ok, here's my topology file: ; Include forcefield parameters #include "ffgmx.itp" #include "lipid.itp"
; Include Lipid Topologies #include "popc.itp" ; Include water topology #include "spc.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include generic topology for ions #include "ions.itp" [ system ] ; Name Berger Membrane in water [ molecules ] ; Compound #mols POP 128 SOL 2460 and here's my ff_dum.itp: ; These constraints are used for dummy constructions as generated by pdb2gmx. ; Values depend on the details of the forcefield, vis. bondlengths and angles ; These parameters are designed to be used with the GROMACS forcefields ; ffgmx and ffgmx2 and with the GROMOS96 forcefields G43a1, G43a2 and G43b1. ; Constraints for the rigid NH3/CH3 groups depend on the hygrogen mass, ; since an increased hydrogen mass translates into increased momentum of ; inertia which translates into a larger distance between the dummy masses. #ifdef HEAVY_H ; now the constraints for the rigid NH3 groups #define DC_MNC1 0.175695 #define DC_MNC2 0.188288 #define DC_MNMN 0.158884 ; now the constraints for the rigid CH3 groups #define DC_MCN 0.198911 #define DC_MCS 0.226838 #define DC_MCC 0.204247 #define DC_MCNR 0.199798 #define DC_MCMC 0.184320 #else ; now the constraints for the rigid NH3 groups #define DC_MNC1 0.144494 #define DC_MNC2 0.158002 #define DC_MNMN 0.079442 ; now the constraints for the rigid CH3 groups #define DC_MCN 0.161051 #define DC_MCS 0.190961 #define DC_MCC 0.166809 #define DC_MCNR 0.162009 #define DC_MCMC 0.092160 #endif ; and the angle-constraints for OH and SH groups in proteins: #define DC_CS 0.23721 #define DC_CO 0.19849 #define DC_PO 0.21603 Thanks for your help! Gard
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