Dear Gromacs users, I would like to use a tabulated potential between the C-alphas of a protein and the virtual sites corresponding to the center of mass of the water molecules. I am also using a tabulated potential to define the interactions between these virtual sites of the solvent. In the mdp file I added the following lines:
energygrps = B CA atoms (B is the water virtual site and atoms includes all the rest of the system) energygrp_table = B B B CA However, I see in the log file that only the file table_B_B.xvg is read, but not the file table_B_CA.xvg (and in fact, I see from the simulation that I don’t have interactions). On the opposite, if I apply the same table to the interactions between CA and atoms of the water molecules (not virtual sites), it works. Does it mean that I cannot apply tabulated potentials between atoms and virtual sites, or that I should change something in the definition of the virtual site? They are defined in an itp file in this way: [ moleculetype ] ; molname nrexcl SOL 2 [ atoms ] ; id at type res nr residu name at name 1 ow 1 SOL ow 1 -0.8476 2 hw 1 SOL hw1 1 0.4238 3 hw 1 SOL hw2 1 0.4238 4 B 1 SOL B 2 0.0000 [ virtual_sites3 ] ; Site from funct a d 4 1 2 3 1 0.05595E+00 0.05595E+00 #ifdef FLEXIBLE [ bonds ] ; i j funct length force.c. 1 2 1 0.1 345000 1 3 1 0.1 345000 [ angles ] ; i j k funct angle force.c. 2 1 3 1 109.47 383 #else [ settles ] ; i j funct length 1 1 0.1 0.1633 #endif [ exclusions ] 1 2 3 4 2 1 3 4 3 1 2 4 In the topology I added these lines: [ atomtypes ] ;name mass charge ptype C6 C12 ow 15.99940 -0.8476 A 2.617065E-03 2.633456E-06 hw 1.00800 0.4238 A 0.000000E+00 0.000000E+00 B 0.00000 0.0000 V 0.000000E+00 0.000000E+00 [ nonbond_params ] ; i j func c6 c12 B B 1 0.000000E+00 1.000000E+00 -- 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.