> Can we use the APR or Umbrella sampling method to study ligand dissociation
events?
Are you asking permission, if so, yes, you can use the APR as in the tutorial (as others mentioned) to look at the free energy of binding and potentially, if lucky, dissect some of the molecular processes of the dissociation process. Can you use APR to see spontaneous dissociation, no. Either you apply biases to see the process of interest (and hope it is representative) or no bias and hope to see it in spontaneous simulation. In spontaneous simulation this is often hard (since the time scales are too long) which is why people apply biases. A difficultly of biases is if the wrong bias is chosen is (which is often difficult to assess) how do you know if correct. The best approach is multiple methods (biased and unbiased) and trying to assess statistical significance noting that there is a very large literature in these areas...
--tec3
________________________________________
From: Rana Rehan Khalid <ray.binm.gmail.com>
Sent: Tuesday, May 25, 2021 4:00 PM
To: AMBER Mailing List
Subject: [AMBER] Umbrella sampling
Dear Amber user
Can we use the APR or Umbrella sampling method to study ligand dissociation
events?
Best
Rehan
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Received on Wed May 26 2021 - 10:30:02 PDT
