Hi,
As I was browsing the literature I found SMD and Umbrella Sampling among the general practices when one wants to get the free energy of the system especially when there is one reaction coordinate…I was reading the papers on SMD and US but I couldn’t find a comparison between two, basically I don’t when you decide to use SMD and when US, can somebody give me any references that compare these two methods? Can they be used interchangeably at all?
I appreciate any help,
Kasra.
Hi,
As I was browsing the literature I found SMD and Umbrella Sampling among the
general practices when one wants to get the free energy of the system
especially when there is one reaction coordinate...I was reading the papers
on SMD and US but I couldn't find a comparison between two, basically I
don't when you decide to use SMD and when US, can somebody give me any
there are *tons* of papers and entire books written on the topic of
free energy calculations. you didn't look properly.
references that compare these two methods? Can they be used interchangeably
at all?
umbrella sampling is effectively steered MD in the limit of
infinitesimal speed. umbrella sampling has the advantage that it is
easily parallelized and it is easy to control the statistical accuracy
(and for each bin independently). steered MD allows you to handle
systems and processes, that cannot be dealt with in umbrella sampling.
axel.
Thank you so much Axel, that was very succinct.
What are your suggested books especially the ones that include SMD and US?
Best,
Kasra.
Thank you so much Axel, that was very succinct.
What are your suggested books especially the ones that include SMD and US?
i don't have the time to do web searches for other people. most books
on statistical mechanics for molecular simulations should include
something. no book will just have the answer to your specific
question. you'll have to spend some time reading and figuring out
things. there should be several detailed articles on SMD and other
free energy methods and their accuracy. i think there is a book on all
kinds of free energy methods edited by christophe chipot
please help yourself.
axel.
Below the book Axel (I think) is citing.
Chipot C, Pohorille A. Free Energy Calculations:
Theory and Applications in Chemistry and Biology.
Berlin/Heidelberg:Springer; 2007.
Carlos
Thank you all.
Kasra.