RE: rule of thumb for dcd sampling frequency?

From: Irene Newhouse (einew_at_hotmail.com)
Date: Tue Mar 22 2011 - 13:00:28 CDT

I'd like to save every picosecond, & for shorter runs I do. I'm interested in slower phenomena at this point, & I'm also at disadvantage due to a creaky internet connection. At the moment, I have to use the unix split command to split my tarballs into 500MB chunks & it's taking me as long to download the files for analysis as it was to run the MD in the first place. I'd love to be able to stride the files down BUT I'm using an older Desmond that's not compatible with the catdcd Desmond decoder AND it lacks manipulate_trj.py, the Desmond utility that accomplishes something similar. If you suggest I update the Desmond personally, I think it means you've not tried to install it. The support staff are working on an update, but it's not there yet. As soon as they crack that, I'll be in much better shape.
 
Thanks for all the suggestions!
Irene
 

Date: Tue, 22 Mar 2011 10:47:29 +0100
From: bdrakuli_at_chem.bg.ac.rs
To: rwoodphd_at_yahoo.com; namd-l_at_ks.uiuc.edu
Subject: Re: namd-l: rule of thumb for dcd sampling frequency?

Richard,

Axel, as always, give best explanation

Branko

On 3/22/2011 12:43 AM, Richard Wood wrote:

Wouldn't saving every picosecond be adequate?

Richard

From: Branko <bdrakuli_at_chem.bg.ac.rs>
To: Irene Newhouse <einew_at_hotmail.com>; namd-l <namd-l_at_ks.uiuc.edu>
Sent: Mon, March 21, 2011 2:13:51 PM
Subject: Re: namd-l: rule of thumb for dcd sampling frequency?

Irene,

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: http://www.ks.uiuc.edu/Research/namd/papers.html#cites, 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 (http://www.ks.uiuc.edu/Research/namd/)

Branko

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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