[gmx-users] error, bug (?) using pbc = no
David van der Spoel
spoel at xray.bmc.uu.se
Wed Aug 17 15:04:27 CEST 2005
On Wed, 2005-08-17 at 10:00 -0230, Jennifer Rendell wrote:
> Dear Fellow Users,
> Following a suggestion made by David van der Spoel in a recent gmx-users
> digest, I tried using pbc = no for my peptide which I am trying to
> restrain to a helical conformation.
> Grompp gave me three warnings:
> 1. Can only use nstype=Simple with pbc=no, setting nstype to Simple
> 2. Tumbling ice-cubes: We are not removing rotation around center of mass
> in a non-periodic system. You should set nstcomm = -1.
> 3. charge non-zero (not a problem)
> and an error:
> ERROR: Twin-range neighbour searching (NS) with simple NS algorithm not
> Does this mean I can't use pbc = no?
> Puzzled, Jennifer
> I am using gromacs 3.1.4.
It might be wise to upgrade, but anyway, you should either change your
cut-offs to a single cut-off rather than twin-range, or use a large box
with the nstype=grid option if you insist on twin-range potentials.
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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