Re: rule of thumb for dcd sampling frequency?

From: Richard Wood (
Date: Mon Mar 21 2011 - 18:43:30 CDT

Wouldn't saving every picosecond be adequate?


From: Branko <>
To: Irene Newhouse <>; namd-l <>
Sent: Mon, March 21, 2011 2:13:51 PM
Subject: Re: namd-l: rule of thumb for dcd sampling frequency?


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
>Irene Newhouse
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