[gmx-users] problem with genconf
albert_sun9 at yahoo.com
Thu Jun 10 17:03:38 CEST 2004
Thanks, David !
How to equilibrate with freshly generated velocities?
David <spoel at xray.bmc.uu.se> wrote:
On Wed, 2004-06-09 at 20:45, Albert Sun wrote:
> Dear Users.
> The problem is solved beause I used the same file name in genconf.
> I have another inquery on genconf. It is said that genconf multiplies
> a given coordinate file by simply stacking them on top of each other,
> like child playing wood blocks. It is OK for positions of atoms.
> However, I found the velocity for all blocks are exactly the same, is
> it correct ?
just equilibrate for a while with freshly generated velocities. if you
have a lot of order in your original system you may need to equilibrate
> Thanks in advance.
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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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