[Chimera-users] REntropy

Paul Buscemi busce004 at umn.edu
Tue May 23 18:10:17 PDT 2017


Thank you Elaine,  This is quite helpful

I was not so concerned with calculating S, or delG,  but more along the line of , as you suggested, the effects and this should be revealed in protein folding as well as adsorption.

Best 
Paul
> On May 23, 2017, at 11:24 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hi Paul,
> The dynamics may reveal entropic effects (does the water have more freedom to move around in one state relative to another state?) but no, the MD tool does not output some entropy value, nor does it calculate free energies, which include entropy.   Some other simulation packages (AMBER etc.) include methods for calculating relative free energies (deltaGs), typically involving very long simulations.
> 
> The AL2CO entropy is something entirely different.  It is a measure of conservation per column in a multiple sequence alignment.
> I hope this clarifies,
> Elaine
> ----------
> Elaine C. Meng, Ph.D. 
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> 
>> On May 22, 2017, at 6:23 PM, Paul Buscemi <busce004 at umn.edu> wrote:
>> 
>> Elaine ,
>> 
>> If yo do not mind giving me a head start on this,    Because I am dealing with polymer conformation  adsorbed onto on surfaces from solution and  entropy can play a huge roll re solvent displacement.   Is there any sort of adjustment / account for entropy in MD ?  I know this is asking a lot of the system.   I saw the mavConservation  - AL2CO program but I do know is this is applicable in this type model..
>> 
>> 
>> Best 
>> Paul
> 




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