Re: running a calculation during simulation

From: Jérôme Hénin (
Date: Tue Oct 21 2014 - 04:03:13 CDT


For parallel processing on many atoms, TclBC might be a good option. What I
don't know is what kind of parallel output you can do with TclBC.


On 21 October 2014 09:52, Ajasja Ljubetič <> wrote:

> Hi,
> Using the colvars module you can write a portion of the coordinates more
> frequently than DCDfreq. (I did this for two atoms, for more it probably
> gets cumbersome).
> Another option is to run the simulation in small chunks with a high
> DCDfreq and then only extract the desired selection using catDCD after each
> chunk is completed. (This will probably be faster than a lot of colvars)
> Best regads,
> Ajasja
> On 20 October 2014 23:08, <> wrote:
>> Hi,
>> I am looking to use the coordinates of a selection of atoms in my
>> simulation at a sampling rate considerably higher than that of the
>> dcdfreq. I was wondering if there was a way to run a tcl script
>> concurrently with the simulation. Specifically, I am trying to calculate a
>> one-dimensional density of atoms averaged more frequently than I am
>> writing all the atoms to the dcd.
>> -Brad

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