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

Rossen Apostolov rpa at mochiron.org
Wed Feb 22 04:54:48 CET 2006

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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