Dear All, I'm using charmm force field for simulation of a protein ligand system. I have read the paper "implementation of charmm in gromacs by Bjelkmar, JCTC' They have used the following set up
coulombtype = PME rcoulomb = 1.2 vdwtype = switch rvdw = 1.2 rvdw-switch = 1.0 Now, with this same set up if I use rlist = 1.2 rlistlong =1.4 It is showing the following warning NOTE 1 [file 02md.mdp]: For energy conservation with switch/shift potentials, rlist should be 0.1 to 0.3 nm larger than rvdw. Now, if I try to increase the rlist as rlist =1.3 Coulomb part is showing warning as *ERROR 1 [file 02md.mdp]:** With coulombtype = PME, rcoulomb must be equal to rlist** If you want optimal energy conservation or exact integration use** PME-Switch* I came across this post in the mailing list http://lists.gromacs.org/pipermail/gmx-users/2013-February/079037.html But the point, if I use rlist=rvdw then the dynamics will not be proper as in the neighbor list updating and energy calculations. Can any one suggest me the best possible use of these parameters? I am using gromacs-4.5.5 for simulations. Thanks, Tarak -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
