On 15 February 2012 21:00, Mark Abraham <[email protected]> wrote:
> On 16/02/2012 12:22 PM, Justin A. Lemkul wrote: > >> >> >> Juliette N. wrote: >> >>> Hi all, >>> >>> I am trying to run simulation in vaccum using the the changes shown >>> below to the usual mdp file. >>> pbc = no >>> >>> ;coulombtype = PME ;vdw-type = Shift >>> ; Cut-offs >>> rlist = 0 rcoulomb = 0 >>> rvdw = 0 >>> >>> nstlist = 0 ns_type = simple >>> >>> Can anyone help me with some short questions please? >>> >>> 1- for pbc=no, I need to comment >>> >>> ;coulombtype = PME ;vdw-type = Shift >>> so it defaults to vdw-type = Cut-off which are not suitable algorithms. >>> Is using cut offs justified for in vacu runs? >>> >>> >> Plain truncations in condensed-phase systems lead to artifacts. Neither >> of those conditions apply here, as you're using infinite cutoffs. >> >> >>> 2- I am not clear about using infinite cutoffs. Why one refers to >>> infinite cutoffs when >>> >>> rlist = 0 rcoulomb = 0 >>> rvdw = 0 ? >>> >>> My understanding is that this settings means zero cutoff i.e no >>> interaction is calculated. Why does this setting refer to infinite rc? >>> >>> >>> >> That's the way the code works. There are various parameters that can be >> set to -1, for instance, and that doesn't mean quantities are calculated >> every -1 steps ;) >> >> Setting cutoffs to zero in this manner mean *all* interactions are >> calculated, not none. Prove it to yourself with a zero-step MD run. The >> nonbonded energy terms will not be zero, as they would in the case that no >> interactions would be calculated. >> >> > Or read about pbc=no in manual section 3.4.9 like I suggested Juliette do > earlier this week... > Thanks Justin and Mark. I think you meant 7.3.9 which I did when you referred me to that. My problem was that I did not expect rc=0 is *just defined* as infinite cutoff in gromacs. To me rc=0 looked more equivalent to no interaction than infinite cutff off (all interactions). And also I dont see why do we need to change rc to infinite. I mean if force fields dictate cutoffs based on a distance where nonbonded interactions are close enough to zero (negligible), what purpose use of infinite cutoff serve? > >
-- 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
