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From: <steinbrt.rci.rutgers.edu>

Date: Thu, 10 Jun 2010 03:23:29 -0400 (EDT)

Hi,

*> Great. Thanks for response. I made myself a simple reaction coordinate
*

*> to start with: the angle between three domains. Calculated that with
*

*> ptraj, and measured min and max values of this.
*

Especially important would be the overlap of both. Plot your histograms

and see if they sufficiently overlap, you need lots of data at every point

along the coordinate.

*> As input to WHAM, I used the measured angles, and 0 as spring constant
*

*> for the biasing potential:
*

*> "wham Pval 74.1 131.5 200 0.0001 300.0 0 angle_metadatafile angle.pmf"
*

*> where 74 and 131 are min and max angles, 200 is the number of bins,
*

*> 0.0001 is the wham convergence tolerance, and 300 is the temperature.
*

Each of your bins will only be .3 degree wide. Look at the point where

both histograms are most sparsely populated. How many data point per bin

would you have? If too few, reduce the number of bins accordingly, or do

you really need such a finely resolved reaction coordinate?

*> Does this sound reasonable in order to get some sort of free energy
*

*> profile as a function of the domain angles?
*

Im no WHAM expert, but that sounds ok to me. You are one stroke of the

'Enter' key away from finding out :-D

*> I guessing I'm a bit off here since you say "by hand", and two-window..?
*

You have two-windows because you have two (endpoint) simulations that

provide you with histograms. I said by hand because Im not sure if WHAM

will accept a zero force constant. All the better if it does.

Kind Regards,

Thomas

Dr. Thomas Steinbrecher

BioMaps Institute

Rutgers University

610 Taylor Rd.

Piscataway, NJ 08854

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Received on Thu Jun 10 2010 - 00:30:03 PDT

Date: Thu, 10 Jun 2010 03:23:29 -0400 (EDT)

Hi,

Especially important would be the overlap of both. Plot your histograms

and see if they sufficiently overlap, you need lots of data at every point

along the coordinate.

Each of your bins will only be .3 degree wide. Look at the point where

both histograms are most sparsely populated. How many data point per bin

would you have? If too few, reduce the number of bins accordingly, or do

you really need such a finely resolved reaction coordinate?

Im no WHAM expert, but that sounds ok to me. You are one stroke of the

'Enter' key away from finding out :-D

You have two-windows because you have two (endpoint) simulations that

provide you with histograms. I said by hand because Im not sure if WHAM

will accept a zero force constant. All the better if it does.

Kind Regards,

Thomas

Dr. Thomas Steinbrecher

BioMaps Institute

Rutgers University

610 Taylor Rd.

Piscataway, NJ 08854

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AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Thu Jun 10 2010 - 00:30:03 PDT

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