Dear gmx-users: I was trying to do a free energy calculation of a charged ligand, according to the paper "Calculation of Absolute Binding Free Energies for Charged Ligands and Effects of Long-Range Electrostatic Interactions ", one of the problems with charged ligands is that the use of a solvent-solvent cutoff causes an overpolarization of the the solvent toward the solute charge, but this can be done by not using any cutoffs at all (If I did not misunderstand it).
In the following, this is my part of mdp parameter for non-charged ligand: ; Neighborsearching and short-range nonbonded interactions nstlist = 10 ns_type = grid pbc = xyz rlist = 1.2 ; Electrostatics coulombtype = PME rcoulomb = 1.2 ; van der Waals vdw-type = switch rvdw-switch = 0.8 rvdw = 0.9 for charged ligand, it is like this: ; Neighborsearching and short-range nonbonded interactions nstlist = 0 ns_type = simple pbc = no rlist = 0.0 ; Electrostatics coulombtype = cut-off rcoulomb = 0.0 ; van der Waals vdw-type = cut-off rvdw-switch = 0.0 rvdw = 0.0 Is this correct for what it means in the paper that by using no cutoff at all? Anyway, I presume that this is correct, and run some free energy calculation, when I used the g_bar to calculate the results, I got the error message like this : Fatal error: Some dhdl files contain only one value (dH/dl), while others contain multiple values (dH/dl and/or Delta H), will not proceed because of possible inconsistencies. So what does it mean? Thank you for answering my questions in advance. Regards Chunxia
-- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
