On 5/10/13 1:55 AM, Shima Arasteh wrote:
Hi,
In Umbrella Sampling method, among mdp settings, there is a section where the
pull code settings are defined in:
pull = umbrella: using a harmonic potential to pull
As it is said that "with US the path of the permeating ion along thereaction
coordinate is sampled using many discrete windows, whereas with SMD the ion is
pulledalong this same reaction coordinate",
I am on a doubt that how the pull code with a harmonic potential works here? I
am little confused.
Would you please giveme a hint to understand it?
To carry out umbrella sampling with the pull code, you restrain configurations
at varying distances with a harmonic potential (see my tutorial for an example,
and the vast body of literature on this topic for the underlying theory). SMD
can be conducted in a number of ways and need not involve a harmonic potential.
The two techniques (US and SMD) are different, but make use of common portions
of code since some aspects are somewhat similar.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
