Re: [gmx-users] RF and TI

But my system is rigid benzene molecule, and all intramolecular interactions are absent. The RF modifies a short-range electrostatic potential. Is it correct for both decoupling scheme and "manual" method? Where is the difference? And what about additive constant (named Crf in the manual, formula 4

[gmx-users] RF and TI

Dear gmx users, I calculated the hydration free energy of benzene molecule two times. First time I used a decoupling method implemented in GROMACS. Second time I performed thermodynamical integration between different topologies of the benzene molecule: non-interacting with media and normal one. Al

[gmx-users] density and intramolecular interactions

Hi everyone, I have a model for liquid benzene. In this model all bonds are treated as harmonic potentials. When I use larger constants for these potentials (to make molecules more planar), the average density of my benzene (from NPT ensemble) becomes lower. Does virial depend on intramolecular int

[gmx-users] Re: RE: question about PME

A and B must be eliminated from the PMF. The question is, whether we have to subtract the true Coulomb energy 1/R (R is the inter-ionic distance) or this term is distorted during the PME computation and must be modified in some way before being subtracted. Thanks in advance for your help,

[gmx-users] question about PME

advance for your help, Alexey Odinokov ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe reques