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From: Yan Li <liyantiger.yahoo.com>

Date: Wed, 8 Aug 2012 10:07:37 -0700 (PDT)

Dear Amber users,

I am trying to calculate PMF with WHAM, and have a question about the spring constant. In Amber manual, it says PMF can be computed using umbrella sampling. And in WHAM input file, the spring constant from umbrella sampling is needed. It looks the spring constant is necessary, but I wonder how the spring constant is used in WHAM after reading WHAM manual.

The first question is that, in many MD trajectories with umbrella sampling, if all time series data have the same spring constant, does the absolute value of the spring constant affect WHAM results? For example, if the spring constant is set to 2 or 4 in WHAM input file no matter what it is in MD, will it generate different energy surfaces?

Another question is that, suppose that I have a very long MD trajectory (long enough to sample) without any constraint, is it possible to calculate PMF from this trajectory? If possible, what should the spring constant be?

It looks like a stupid question. I would very appreciate that you could correct my misunderstanding. Thank you for your time.

best wishes,

Yan

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Received on Wed Aug 08 2012 - 10:30:03 PDT

Date: Wed, 8 Aug 2012 10:07:37 -0700 (PDT)

Dear Amber users,

I am trying to calculate PMF with WHAM, and have a question about the spring constant. In Amber manual, it says PMF can be computed using umbrella sampling. And in WHAM input file, the spring constant from umbrella sampling is needed. It looks the spring constant is necessary, but I wonder how the spring constant is used in WHAM after reading WHAM manual.

The first question is that, in many MD trajectories with umbrella sampling, if all time series data have the same spring constant, does the absolute value of the spring constant affect WHAM results? For example, if the spring constant is set to 2 or 4 in WHAM input file no matter what it is in MD, will it generate different energy surfaces?

Another question is that, suppose that I have a very long MD trajectory (long enough to sample) without any constraint, is it possible to calculate PMF from this trajectory? If possible, what should the spring constant be?

It looks like a stupid question. I would very appreciate that you could correct my misunderstanding. Thank you for your time.

best wishes,

Yan

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

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

Received on Wed Aug 08 2012 - 10:30:03 PDT

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