Re: rule of thumb for dcd sampling frequency?

From: Axel Kohlmeyer (
Date: Mon Mar 21 2011 - 14:12:00 CDT


On Mon, Mar 21, 2011 at 2:26 PM, Irene Newhouse <> wrote:
> What are some rules of thumb for trajectory sampling? For instance, if
> you're intending to simulate for 100nsec, how many frames sample the time
> span adequately? 1 microsec? Pointers to references would be greatly
> appreciated.

it is not the total length of the trajectory that matters,
but the frequency/speed of the events that you want
to study. in a way similar to how the fastest frequency
in your system determines a suitable time step.

i personally have been looking at rather slow processes,
but needed to store data more often because of rather
large amplitude fast vibrations that needed to be averaged
out during analysis.

for projects where it is difficult to predict, it might be
beneficial to store at first rather often (say every ps)
and then do the part of the analysis that needs frequent
data right away (and in blocks) and then use catdcd
to compress ot 1/10th or even 1/100th. and keep only
those trajectory files around permanently.


> Thanks!
> Irene Newhouse

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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