[gmx-users] Position restrain in umbrella sampling

Justin Lemkul jalemkul at vt.edu
Wed Jun 6 17:31:26 CEST 2018

On 6/6/18 11:18 AM, rose rahmani wrote:
> Hi,
> I'm doing umbrella sampling for different distances of amino acid from
> surface.
> I know that dear Justin warns people that position restraint was for that
> specific situation in the article mentioned in tutorial and ....
> I know it doesn't make a sense in my system too in PULLING. But i don't
> understand why it's not usable for the rest; i mean in nvt_umbrella for
> each window and conformation. I extract different conformations to show the
> potential of mean force on that exact distance. So if i don't use position
> restraint for AA in for example 0.5nm distance from surface so i can't
> claim that this nvt_umbrella run is showing the system manner in a
> situation that AA is about 0.5 from surface because without position
> restraint(for AA) the AA can be anywhere in box ... . ( i should mention
> that surface is frozen in my system)Would you please correct me if i'm
> wrong?

You shouldn't be layering biases upon biases to try to force a certain 
behavior. It is possible to combine various restraints as long as the 
resulting PMF is corrected for these effects.

For each window, you define an origin of the umbrella potential. If 
that's 0.5 nm and the specified COM distance (or whatever) does not 
oscillate about this value, then there are two possibilities: (1) Your 
force constant is not large enough or (2) the physical forces in your 
system are such that it is not physically reasonable for the entities to 
exist at that interaction distance.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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