[gmx-users] NMA problem (again and again!)

[Fabrizio Mancinelli]

Hi Rossen,

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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