msnayeem at gmail.com
Tue Feb 28 06:59:20 CET 2012
Thanks. But Does that mean that I should look in pullf.xvg of each window
and see whether the value is converged or not. If not then I should extend
On Sat, Feb 25, 2012 at 12:05 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> shahid nayeem wrote:
>> My protein complex interface has a hydrophobic core and on each side of
>> this core at the edge are two hydrogen bonds. The Hydrogen bond on one side
>> is between Arg and Asp and another side it is between Arg and Glu. Its
>> experimental Kd is in nanomolar regions. How should I decide the length of
>> the simulation required in each window with this information.
> As you would any other system. Look for convergence of observables of
> interest. Your PMF alone suggests insufficient sampling for these
> simulations, so as I've said several times, you probably need longer
> simulations to do so, but you can start by examining the physical
> properties of each window. What you're looking for is up to you, based on
> your knowledge of the system at hand.
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<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 gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users