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From: Ramin Salimi <ramin.salimi01.utrgv.edu>

Date: Wed, 17 May 2017 08:24:54 +0000

Hi Amber Users

I have a few questions about calculating the variance and error of the Steered MD/Jarzynski Method:

1- Having completed the SMD, how to calculate the second cumulant expansion to see how different it is from the full Jarzynski average?

2- How should I check the variance between the replicates at the end of the pull? Does it mean that I should take the arithmetic average of the work values, corresponding to different iterations, at each extension and then calculate the variance corresponding to the set of work values for a particular extension? If yes, then we would have many variances corresponding to a particular extension, which does not make much sense to me.

3- Can we compute the variance, or standard deviation, and second order cumulant expansion in Amber? I mean does it have the capability of computing these as well?

4- How different is it from the Jarzynski method, that basically works on a reaction coordinate i.e. the distance between the atoms or groups of atoms, when we use ntr to freeze one atom or a group of atoms, and pull the other end with a different potential? I mean what difference does it make in results? which one is better to use? I would want to learn how different the physics of the problem would be for I am used to see only constant force constants in SMD.

I would really appreciate any help.

Regards

Ramin

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Received on Wed May 17 2017 - 01:30:04 PDT

Date: Wed, 17 May 2017 08:24:54 +0000

Hi Amber Users

I have a few questions about calculating the variance and error of the Steered MD/Jarzynski Method:

1- Having completed the SMD, how to calculate the second cumulant expansion to see how different it is from the full Jarzynski average?

2- How should I check the variance between the replicates at the end of the pull? Does it mean that I should take the arithmetic average of the work values, corresponding to different iterations, at each extension and then calculate the variance corresponding to the set of work values for a particular extension? If yes, then we would have many variances corresponding to a particular extension, which does not make much sense to me.

3- Can we compute the variance, or standard deviation, and second order cumulant expansion in Amber? I mean does it have the capability of computing these as well?

4- How different is it from the Jarzynski method, that basically works on a reaction coordinate i.e. the distance between the atoms or groups of atoms, when we use ntr to freeze one atom or a group of atoms, and pull the other end with a different potential? I mean what difference does it make in results? which one is better to use? I would want to learn how different the physics of the problem would be for I am used to see only constant force constants in SMD.

I would really appreciate any help.

Regards

Ramin

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

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

Received on Wed May 17 2017 - 01:30:04 PDT

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