[gmx-users] NMA problem (again and again!)
rpa at mochiron.org
Wed Feb 22 04:54:48 CET 2006
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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