On 15 February 2012 23:05, Mark Abraham <mark.abra...@anu.edu.au> wrote:
> On 16/02/2012 2:08 PM, Juliette N. wrote: > > > > On 15 February 2012 21:00, Mark Abraham <mark.abra...@anu.edu.au> 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). > > > Sure, but reading the documentation is usually a better idea than making > assumptions :) > > The underlying reason for this behaviour is that it is much easier for the > person writing the code to have one parameter that occasionally has a > "special" meaning when it takes a nonsense value (like rc<=0) then it is to > have a slew of parameters that have to be managed when they are input (and > checked, and documented) and then possibly passed through a cascade of > functions (lots of bureaucracy and chances to make errors) before they are > used. The alternative costs the programmer more time. In an ideal world > there would be an infinite amount of such time, but given the amount most > people are prepared to pay for scientific software, that time is severely > limited. > > > 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? > > > Efficiency, like I said in the first post in this thread. Given that your > force field was parametrized with given cut-offs for the condensed phase, > to what purpose do you wish to calculate in vacuo? The perturbation from > calculating in vacuo will be much larger than the perturbation from the use > of infinite cut-offs. > Thank you. I am looking at potential of a single molecule in vacu for heat of vap purposes at different temperatures by changing ref_temp and gen_temp for each run. > > Mark > > -- > 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 > -- Thanks, J. N.
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