Re: [AMBER] MMPBSA per residue decomposition - Calculation speed

From: David A Case <david.case.rutgers.edu>
Date: Thu, 8 Apr 2021 08:17:48 -0400

On Wed, Apr 07, 2021, Kashyap, Jatin wrote:
>
>I had performed the calculation again by splitting the 1-10 trajectory into
>1-3 and 4-10. And results changed by +/-1% from older values but they are
>not adding up lenearly.

This depends on what you mean (and I mean!) by "linear". Each snapshot
contributes equally (linearly) to the final answer for energy terms. So, if
you have 3 snapshots in one bucket, and 7 in the second bucket, you would
need to weight the buckets by the number of snapshots they contain.

With only 10 frames, you can do the entire calculation (say for one energy
component) completely by hand, and compare to what the program yields. This
way, you will make sure you understand what is going on under the hood.

....dac


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Received on Thu Apr 08 2021 - 05:30:03 PDT
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