Re: [ESPResSo] Checkpoint- NPT Simulations

[Axel Arnold]

On Thursday 19 November 2009 09:43:25 pm Salvador Herrera Velarde wrote:
> Hi,
>
> I have a problem when I want to restart a simulation from a checkpoint
> (NVT), althought the same situation is  present with NPT simulations.
>
> In our cluster we have a time-limit to run simulations (the job is
> automatically killed), so from time to time I need to restart the
> simulations from the last checkpoint. But even when the simulation was
> running fine before was killed, when I tried to restart the simulation it
> crashes and complains about floating point exception.
>
> The same problemm occurs for NPT simulations, but in this case the problem
> is worst because for any system after the thermalizacion (NVT and capped
> forces) the system crashes every time.
>
> Any suggestion how to fix this?

How do you read back the checkpoint? The checkpoints contain most of the 
internal state of Espresso, but not the state of the Tcl Interpreter. 
Therefore, you need to be careful that you enter your integrate loops at the 
right time, where you wrote the snapshot. If you for example again start with 
the equilibration, but with the parameters of the snapshot, your simulation 
will probably crash. First thing you should do therefore is to check that 
after reading back your checkpoint, the system is set up as you need it 
(thermostat, integrator, bonds, potentials).

Axel

-- 
Dr. Axel Arnold
Schloss Birlinghoven
53754 St. Augustin, Germany
Tel. +49 2241 14 2575