[gmx-users] -ndec 30
Nguyen Hoang Phuong
phuong at theochem.uni-frankfurt.de
Wed Nov 12 17:55:01 CET 2003
> 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 considered (and tried?) tpbconv? That will allow you to take
> the coordinates and velocities from a .trr file and write it to a .tpr
> file in full precision (either single or double, depending on your
> files and the program, i.e. all double in your case).
the problem is that I would like to change the coordinates of some atoms
in the last step of the fisrt run before using this for the next run. That
why I convert the trr file to gro file (g96 as David said is not possible
for me because it doesn't contains velecities) and change coordinates in
this gro file. How can I keep the precision of the velocities in this gro
file as same as in the trr file?
Thanks for any help.
> _____________ _______________________________________________________
> | | |
> | _ _ ___,| K. Anton Feenstra |
> | / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
> |( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands |
> | \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 |
> | | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/ |
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