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Re: [ESPResSo-users] continue an interrupted simulation which used pepti

From: pdam bright
Subject: Re: [ESPResSo-users] continue an interrupted simulation which used peptideB
Date: Thu, 28 Feb 2013 17:23:45 +0330

Sorry, from the last pdb file!

Thanks Stephan,

My main question is how I can feed the last configuration before interruption (the last pdb file), to the codes of peptideB? As you know there is two main tcl files peptidebuilder.tcl and mypeptide.tcl. The second file needs the sequence of my peptide not the position of atoms in the chain!

Thanks again,

On Thu, Feb 28, 2013 at 5:12 PM, Stefan Kesselheim <address@hidden> wrote:
Hi Pee,

On Feb 28, 2013, at 2:35 PM, pdam bright <address@hidden> wrote:

> Dear all,
> I am using peptideB to simulate a peptide. But my computer has been shut down and I have to run it from the beginning. Is there any way to continue the simulation from where it has been interrupted using the last VMD file?

In principle this might be possible, but surely is not intended that way. A good method for continue simulations is using the blockfile format to regularly store the necessary particle data (and other parameters) and write the simulation script in two variants: One for the initial setup and one that allows to continue the simulation from the data stored in a block file.
We do not support "checkpointing" in the sense that you can have an automatically created file that contains everything necessary to continue running. One reason is that this would include the necessity to store the full state of the TCL interpreter.

If it is just one afternoon of computation, it is probably easier to re-run the simulation :-). The particle positions can however be extracted from a vtf file, if necessary, but that is manual work.

Cheers and good luck,

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