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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: Tue, 5 Mar 2013 15:18:04 +0330

Dear Tristan and Stephan,

Many thanks for your help!

Seems -pdb flag works perfectly :)


On Thu, Feb 28, 2013 at 5:51 PM, Tristan Bereau <address@hidden> wrote:
Hi Pee,

The easiest is to feed the last PDB file you've outputted to the
peptideB command (using the -pdb flag to load that file). From what I
remember, the same should hold from REMD, though all replicas will
load that particular file (I haven't implemented a routine to load
different PDB files for different replicas).

Let me know if that's still unclear.


On Thu, Feb 28, 2013 at 2:53 PM, pdam bright <address@hidden> wrote:
> 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,
> Pee
> 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,
>> Stefan

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