[gmx-users] NMA problem (again and again!)
fabrizio.mancinelli at unina2.it
Wed Feb 22 11:39:56 CET 2006
actually that's exactly what I did: cut-off further as it were infinite. I
didn't tried SO FAR yet (will be next attempt), did it work with your
protein? By the way, it looks a bit deceptive ;-)
Alle 04:54, mercoledì 22 febbraio 2006, Rossen Apostolov ha scritto:
> Hi Fabrizio
> I figured it out!
> Fabrizio Mancinelli wrote:
> > Hi Rossen,
> > before claiming a bug I'm looking for (hopefully) a mistake by myself!
> > I tried to minimize further (by using l-bfgs) the cg-minimized structure,
> > but I got the same error. Maybe the structure is not properly minimized
> > yet? Another problem could be inferred to the electrostatic treatment.
> You were right about the electrostatics:)
> The problem was that for NMA of huge system we need cut-off
> electrostatics otherwise we can't use sparse matrix.
> But for minimization we'd better use no-cutoff otherwise
> it can't minize sufficiently, interactions getting in and out of
> the list. That's where we were getting the big force - we were changing
> the cutoff logic (at least in my case)
> So what I did is I used huge cut-off for both minimization and NM,
> so that it includes all the atoms, as if there is no cut-off
> and it works like charm...umm,well, gromacs...:)
> nstlist = 1000
> ns_type = simple
> rlist = 35.0
> coulombtype = Shift
> rcoulomb_switch = 32.0
> rcoulomb = 34.0
> vdw-type = Shift
> rvdw_switch = 32.0
> rvdw = 34.0
> pbc = no
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