[gmx-users] (no subject)

[Xavier Periole]

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
   
----------------------------------------------