[gmx-users] (no subject)
Xavier Periole
x.periole at chem.rug.nl
Tue Nov 9 12:52:54 CET 2004
Hector Mrz-Seara Monne wrote:
> hello, the system I'm working on seems to have the problem of
> presenting strong forces during the dynamics that finish in the
> explode of the system. Just to clarify what Xavier
> (x.periole at chem.rug.nl) wrote, how is possible to have a different
> behavior, even a slightly different route, if you start for o point of
> the dynamics that goes thougth the same path that does that has
> explode out your system. Do you regenerate the velocities or something
> similar? or is more like playing with intrinsic round errors of the
> computer?
>
You got different solutions:
1) you generate new velocities to give to a conf before the exploxion
point. It that case
the simulation can not be considered as the continuation of previous
one. It is a different
simulation. But it will be correlated to the previous one because you
used a conformation
taken out fron the trajectory.
2) you can use trjconv -f traj.trr -dump XXXX to extract the
conformation and velocities
of the simulation at the time XXXX. create a new topol.tpr using those
velovities. The
loss precision and the caotic behaviour of the propagation of your
system will give you
a slightly different route and the system may not explode. You can check
the deviation of
the two simulation by choosing a time long enought before the explotion
and plot any
value (rmsd, energies, ...) and see that the two simulations diverge.
3) you can use the tpbconv -f traj.trr to extract the last frame of the
traj.trr and resend your
run. You'd observe the same behavior of the point 2).
May be other solutions are possible ...
XAvier
--
----------------------------------------------
Xavier Periole - Ph.D.
Dept. of Biophysical Chemistry / MD Group
Univ. of Groningen
Nijenborgh 4
9747 AG Groningen
The Netherlands
Tel: +31-503634329
Fax: +31-503634800
email: x.periole at chem.rug.nl
web-page: http://md.chem.rug.nl/~periole
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