**From:** Jeff Comer (*jeffcomer_at_gmail.com*)

**Date:** Tue Sep 01 2015 - 08:40:14 CDT

**Next message:**Brian Radak: "LJcorrection + switching?"**Previous message:**Dr. Eddie: "Sampling frequency"**In reply to:**Dr. Eddie: "Sampling frequency"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Hi Eddie,

This answer might be too simplistic, but in general you want to sample with

a period on the order of the correlation time of the process you're

studying. This correlation time can be quantified by computing the

autocorrelation function of the quantity of interest. If your samples are

taken with a period much shorter than the correlation time, they contain

redundant information and are occupying more disk space than is necessary.

If your samples are taken at a period much longer than the correlation

time, then you are throwing away perfectly good samples and doing more

computation than necessary to get a precise average.

The correlation time is a guide for doing things like calculating the mean

number of water molecules inside of a cavity (you want a dcdFreq just a bit

shorter than the typical time for molecules to enter and leave the cavity,

which could be ~ns) or calculating the mean force on a solute molecule in

solution (for small solutes the force is correlated on the ~50 fs

timescale).

Practically speaking, it sometimes happens to me that I use a dcdFreq of,

say, 20000, to save disk space, but later I realize that I want to analyze

something that takes place on a faster timescale. So it's often best to

choose a dcdFreq lower than what you think you will need. One option is to

sample just one or a few particular variables with high time resolution,

using Colvars and a small colvarsTrajFrequency. Of course if you later

decide you're interested in another variable, you have to go to the dcd.

Regards,

Jeff

–––––––––––––––––––––––––––––––––––———————

Jeffrey Comer, PhD

Assistant Professor

Institute of Computational Comparative Medicine

Nanotechnology Innovation Center of Kansas State

Kansas State University

Office: P-213 Mosier Hall

Phone: 785-532-6311

On Mon, Aug 31, 2015 at 2:02 PM, Dr. Eddie <eackad_at_gmail.com> wrote:

*> Hello all,
*

*> I have a simple question which I know does not have a simple answer: what
*

*> is the largest sampling frequency (dcd output) I need?
*

*>
*

*> I'm looking for any theoretical work on how to know when: 1) the system
*

*> has converged 2) the sampling rate of the system is sufficiently small to
*

*> NOT alias too much information?
*

*>
*

*> I understand in work with conformational changes in the protein this is
*

*> not an issue. However, for those working on studying the steady-state
*

*> behaviour, how do you tell when your system has a "good" sampling of the
*

*> conformational space so you can extract statistically relevant information
*

*> from it? My goal is to understand this for regular MD so that In can use
*

*> replica exchange which (hopefully) will give the same information in less
*

*> time.
*

*>
*

*> Any references or help would be very helpful!
*

*> Thanks,
*

*> Eddie
*

*>
*

**Next message:**Brian Radak: "LJcorrection + switching?"**Previous message:**Dr. Eddie: "Sampling frequency"**In reply to:**Dr. Eddie: "Sampling frequency"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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