[gmx-users] un-coupled simulations and traj recovery

Giorgos Karvounis gk237 at cam.ac.uk
Wed May 14 10:59:00 CEST 2003

So, i am using un-coupled simulations and try to minimise the energy
> drift (... not very successfully i have to say!)
> It is very important for us to reproduce the trajectories... This is
> we are using PME.
> Do you think is there another way of doing it?

Why do you need this exact reproduction? Could you also write out very
many frames, or would that simply be too much data?



Dear Anton,

we need this reproduction because we want to go back to a specific frame
of a very long simulation (e.g. 40 ns) and look at this frame in detail.
We are doing a kind of analysis on the chaotic motion of the
trajectories .(ref.  D. Nerukh, G. Karvounis, and R. C. Glen, J.
Chem. Phys. 117, 9611 2002)...
If we wanted to save every possible step, we would need a really huge
disk. Instead , we were hoping to be able to reproduce the specific
frames eg, if something was happening between frames 5 and 6, of 10000
steps each, we could go there, reproduce the simulation and get all
10000 steps that we need. Until now, the only way to do this , i think,
is using uncoupled  PME and pay the cost of energy and temperature
...Until we decide to try  hacking the code (...again...).



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