[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]
Re: [ESPResSo-users] continue an interrupted simulation which used pepti
Re: [ESPResSo-users] continue an interrupted simulation which used peptideB
Thu, 28 Feb 2013 15:21:47 +0100
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
> 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,