Re: running a calculation during simulation

From: Ajasja Ljubetič (
Date: Tue Oct 21 2014 - 02:52:21 CDT


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,

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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