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[ESPResSo] Restarting a Simulation

From: Salvador Herrera Velarde
Subject: [ESPResSo] Restarting a Simulation
Date: Thu, 08 Apr 2010 15:05:43 -0500

Hi All,

First of all, thanks to ALL users and developers for your time and help with all my questions.

I using mbtools to run  a simulation which contains a large chain of monomers among other molecules.

I want to restart the simulation with different conditions; to save the actual configuration I was using the command:
polyBlockWrite "$outputdir/$ident.[format %04d $j].gz" {time box_l npt_p_diff } {id pos type v f molecule}

Then, I used the generated file to restart the simulation. However,  when I visualized the snapshots in VMD, there are many bonds spanning along the  box simulation. I think this is an effect of the periodic boundary conditions. To fix the problem I tried to fold the positions:
polyBlockWrite "$outputdir/$ident.[format %04d $j].gz" {time box_l npt_p_diff } {id folded_position type v f molecule}

But still the same problem.

Does anybody has an idea of how to fix the problem?

Thanks a lot for,


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