Re: rule of thumb for dcd sampling frequency?

From: Branko (
Date: Mon Mar 21 2011 - 14:13:51 CDT


This strongly depend on what you planed to do with your output - i.e
which type of analysis you want to do on your output. The best way to
find most suitable sampling is to find how other sampled their systems
looking on elements common to analysis of their systems and that which
you planed At first 100 ns is very long, so maybe better to divide your
simulation on phases - if you apply any biasing method carefully read
NAMD ug before this. Second point is size of your system - contribute
to the size of trajectory, especially if system is big and trajectory
long. So according to my knowledge, the best way is to look on already
published references and compare with your system and your need. God
point to begin is:, providing that
you are already skilled in setting-up simulation and in analysis of
output, in this respect the good way is to pass NAMD tutorials that can
be found on the NAMD main web-page (


On 3/21/2011 7:26 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.
> Thanks!
> Irene Newhouse
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