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

[Fabrizio Mancinelli]

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. Following 
David's suggestion, I applied non-cutoff treatment (molecule's in vacuum):

nstlist = 5
ns_type = simple
pbc = no
rlist = 2.5
coulombtype = shift
rcoulomb-switch = 1
rcoulomb = 2
vdwtype = shift
rvdw-switch = 0
rvdw = 1

Maybe I put wrong values for the parameters or their combination doesn't make 
sense; I accept suggestions!

Unfortunately I'm afraid it's not possible to compare with older versions, 
because they don't support sparse matrix representation (my molecule is quite 
big).

Fabrizio

Alle 06:22, martedì 21 febbraio 2006, Rossen Apostolov ha scritto:
> David van der Spoel wrote:
> > fabrizio.mancinelli at unina2.it wrote:
> >> Hello all,
> >> I've got 2 more question about normal modes analysis.
> >>
> >> 1) at the end of the minimization step, I got a value of about e-04
> >> for Fmax. But, when the mdrun(nm) step starts, it says that Fmax is
> >> about e+02. What could have been happened?
> >
> > Did you use the trr as input for the coordinates in the NM?
>
> I also have the same problem even when using the .trr file.
> The precision for the coordinates in the .tpr input file seems correct
> though.
>
> Fabriziio, did you find a solution?
> Or is this a bug in 3.3 ? I haven't tried older versions...
>
> Rossen
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