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@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@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