[gmx-users] -ndec 30
Nguyen Hoang Phuong
phuong at theochem.uni-frankfurt.de
Tue Nov 11 18:52:01 CET 2003
On 11 Nov 2003, David van der Spoel wrote:
> On Tue, 2003-11-11 at 12:52, Nguyen Hoang Phuong wrote:
> > Dear All,
> > I did run the simulation for 100ps and I would like to continue for
> > another 100ps. In the second run, the input file of coordinates and
> > velocities are taken from the first trajectory with the option -t when
> > running grompp.
> > Alternatively, I use trjconv to convert the last snaphshot of the first
> > trr file to the gro file with the option -ndec 30 (30 number of decimal
> > place) to make sure that the precision of this file is as high as that of
> > trr file. If I start the second run from this gro file then the
> > simulation is crashed. If -ndec 6 or -ndec 15 etc. then OK. Thanks in
> > advance for any explainations.
> have you looked at the gro file? Is it OK? Are the first decimals the
> same as in the -ndec 6 case?
yes, they are the same. I know why the simulations are crashed.
Using (trjconv -ndec 30 -o xx.gro) I got a file name xx.gro and then do
(trjconv -f xx.gro -ndec 30 -o xx.trr) I got the file xx.trr. The
simulations starting with xx.trr are crashed because the coordinates and
velocities in this file are not correct (containning some strange
Does anyone know the reason?
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> David van der Spoel, PhD, Assist. 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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