[gmx-users] Electrostatics and VDW
dmobley at gmail.com
Fri Jan 27 17:55:11 CET 2006
Sorry. I was in a hurry and made a typo. With PME, you don't have to have
rlist>rcoulomb. PME, of course, is only for coulomb interactions, so it has
no bearing on how big rvdw has to be.
It turns out that you have to have rvdw>rlist with vdwtype=cutoff, as
GROMACS is telling you. But I'm not sure that cutoff vdw interactions is
really the best bet, as that means the potential changes discontinuously. We
tend to prefer switched vdw, which has the additional side-effect that you
don't have to have rvdw>rlist.
On 1/27/06, Una Bjarnadottir <una.bjarnadottir at ucd.ie> wrote:
> Dear all,
> Thank you David for your reply,
> Now when I try to use rvdw = 1.0 and rlist 1.1 and rcoulomb = 1.0 I get
> the error; With vdwtype = Cut-off,rvdw must be >= rlist.
> I don't have any rvdw-switch or rcoulomb-switch
> I'm using version 3.2.1 and I thought it had been fixed according to the
> discussion on the list.
> Is there some trich that one has to do to have rlist>rvdw?
> Best wishes to everyone, Una
> > With PME, you don't have to have rlist<rvdw. You might, however, want to
> > have rlist slightly larger than rvdw. You don't have to, but since the
> > neighbor list is only updated every nstlist steps, if rlist is the same
> > rvdw, you can run into the situation where an atom has moved inside the
> > cutoff in a couple of steps, but your calculation doesn't realize it has
> > moved inside the cutoff until after nstlist steps. You can solve the
> > problem, of course, by using nstlist=1, but that could slow things down
> > lot, so it may be better to simply use, say, rlist=1.1 and rvdw=1.0 so
> > appear in the neighbor list before getting counted for vdw interactions.
> > David
> > On 1/24/06, Una Bjarnadottir <una.bjarnadottir at ucd.ie> wrote:
> >>Dear all,
> >>Just to have the content of this discussion clear
> >>and all other discussion on this matter.
> >>When using coulombtype = PME and vdw-type = Cut-off is it alright to
> >>have the;
> >>rlist=rvdw=rcoulomb = 1
> >>rvdw-switch=rcoulomb-swithc = 0
> >>Or does it have to be;
> >>rlist=rcoulmb = 0.9 and rvdw = 1.4
> >>Is the 2nd thing only for cut-off but not for PME?
> >>Thanks in advance for any replies, this is confusing me a lot.
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