Dear Gromacs users, I am trying to use CHARMM27 taking the simulation conditions of two recent articles as guides in optimizing the simulation parameters. (DOI: 10.1021/ct900549r and DOI: 10.1021/jp101581h). -- Both are using PME for electrostatics and I am planning to do that too -- Both have rcoulomb = 1.2 (this value is optimal for CHARMM27 force field as mentioned) -- In the second paper, they have explicitly assigned rvdw = 1.2 (this value is also optimized for CHARMM27 force field) and they assigned the NS rlist = 1.2 because as I understand, using PME as a coulombtype requires rcoulomb to be equal to rlist. I have no problem following up until now and it seems that (rlist = rcoulomb = rvdw = 1.2) presents the best combination of cut-offs for using (coulombtype = PME and vdwtype = cut-off) along with CHARMM27 -- What I can't get is that in the first paper, they mentioned the following "van der Waals interactions were switched off between 1.0 to 1.2 nm" what does that mean in terms of cut-offs and vdwtype? Does that mean vdwtype = switch, vdw_switch = 1, rvdw = 1.2 ? and if this is what is meant, then rlist has to be 0.1-0.3 larger than rvdw to accomodate for the size of the charge groups as mentioned in the manual and accordingly, we can't keep rcoulomb = 1.2 because rcoulomb must be equal to rlist to allow using PME. I am sure I miss something or I misunderstand the above statement (colored red). I would really appreciate any help by explaining the above statement (colored red) in the context of using CHARMM27 force field with optimized rvdw and rcoulomb both equal to 1.2 nm and using PME for electrostatics. Thanks Hassan
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