hello out there, i'm trying to simulate a receptor ligand system in order to extract intermolecular non-bonded interaction energies (vdw/coulomb) and apply the linear interaction energy model.
which parameter settings do you recommend for highly accurate results? up to now, i had chosen (copied from somewhere :) rlist = 1.2 vdwtype = shift rvdw = 1.0 rvdw-switch = 0.9 coulombtype = PME-Switch ; PME rcoulomb = 1.1 resulting in LJ-14 = 0, and Coulomb-14 = 0 (which i "intuitionally" prefer to LJ-SR and Coulomb-SR). i have a box of 8.1857 x 8.1857 x 8.1857 nm. Is it helpful to increase rcoulomb and rvdw up to e.g. 8.0 and rvdw-switch up to 4.0 or/and should i take vdwtype=cut-off instead of shift?? what's the difference? how can i get my LJ-14/Coulomb-14 terms? can anyone provide a well-working combination of parameter settings for non-bonded interactions within a system as described above? that's quite a lot questions, i know. gromacs says: "Refer to the primary literature for your of choice for the recommended settings". However, i couldn't find any recommondations for ffamber99 (ffamber99sb is what i use) in the pdf documents provided with the amber port's download. thanks a lot in anticipation vedat -- gmx-users mailing list [email protected] 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 requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
