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

Date: Wed, 17 May 2017 17:21:41 +0000

Thanks Hannes

You are correct, but I thought that there might be some numerical mysterious way to calculate the error.

But what about the other question that I posed:

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.

When we create the input files for SMD, or nmropt, we should put at least two atoms for iat, but what this case that hold one end with ntr flag? How do we prepare the input file to pull the other end?

Thanks

Ramin

________________________________

From: Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk>

Sent: Wednesday, May 17, 2017 4:12:44 AM

To: amber.ambermd.org

Subject: Re: [AMBER] Statistically estimating the error and data reliability for Jarzynski Method

On Wed, 17 May 2017 09:00:54 +0000

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

*> Hi Hannes
*

*>
*

*> You, in fact, are right since the free energy difference is equal to
*

*> the average work plus the second cumulant expansion, but we do not
*

*> have the free energy difference so amongst the three quantities, we
*

*> only have the average work, not either the variance or the free
*

*> energy difference???
*

The equality only holds when the distribution of the work values is a

Gaussian which e.g. when you operate in a near-equilibrium regime, see

for instance https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.pnas.org%2Fcontent%2F100%2F22%2F12564.long&data=02%7C01%7Cramin.salimi01%40utrgv.edu%7Ccab39f1350dd4d37b6fa08d49d051aa3%7C990436a687df491c91249afa91f88827%7C0%7C0%7C636306092629589944&sdata=xTpWUI9GxYok9YM0GRop1UfrLzx%2FNu0ZvMi6WJTc6g8%3D&reserved=0 .

The variance here is the variance of your work values! E.g. paste all

work values that you have received from N simulations into a spread

sheet and ask it to compute the sample variance (like the function

var.S in Excel/LibreOffice calc) from this data. That's really just

standard statistics.

Cheers,

Hannes.

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Received on Wed May 17 2017 - 10:30:02 PDT

Date: Wed, 17 May 2017 17:21:41 +0000

Thanks Hannes

You are correct, but I thought that there might be some numerical mysterious way to calculate the error.

But what about the other question that I posed:

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.

When we create the input files for SMD, or nmropt, we should put at least two atoms for iat, but what this case that hold one end with ntr flag? How do we prepare the input file to pull the other end?

Thanks

Ramin

________________________________

From: Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk>

Sent: Wednesday, May 17, 2017 4:12:44 AM

To: amber.ambermd.org

Subject: Re: [AMBER] Statistically estimating the error and data reliability for Jarzynski Method

On Wed, 17 May 2017 09:00:54 +0000

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

The equality only holds when the distribution of the work values is a

Gaussian which e.g. when you operate in a near-equilibrium regime, see

for instance https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.pnas.org%2Fcontent%2F100%2F22%2F12564.long&data=02%7C01%7Cramin.salimi01%40utrgv.edu%7Ccab39f1350dd4d37b6fa08d49d051aa3%7C990436a687df491c91249afa91f88827%7C0%7C0%7C636306092629589944&sdata=xTpWUI9GxYok9YM0GRop1UfrLzx%2FNu0ZvMi6WJTc6g8%3D&reserved=0 .

The variance here is the variance of your work values! E.g. paste all

work values that you have received from N simulations into a spread

sheet and ask it to compute the sample variance (like the function

var.S in Excel/LibreOffice calc) from this data. That's really just

standard statistics.

Cheers,

Hannes.

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=02%7C01%7Cramin.salimi01%40utrgv.edu%7Ccab39f1350dd4d37b6fa08d49d051aa3%7C990436a687df491c91249afa91f88827%7C0%7C0%7C636306092629589944&sdata=l0FgNKHHkz2FezT4GzbBmtC0G%2BSPJ%2FIF25lc4OmCU8g%3D&reserved=0

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Received on Wed May 17 2017 - 10:30:02 PDT

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