[gmx-users] Re: Re: Re: Re: Re: Re: Re: Re: umbrella potential

Justin A. Lemkul jalemkul at vt.edu
Thu Oct 8 18:55:45 CEST 2009

Stefan Hoorman wrote:
> Hello. Finally came back with the results. Let me again remind you of 
> what we were talking about. I wanted to obtain the PMF pulling my ligand 
> out of the protein using umbrella sampling and WHAM. After several 
> recomendations you asked me to try and simulate the pulling in a one 
> coordinate fashion. So I have again re-equilibrated my system in such a 
> configuration so that the pulling now is made only in the Y axis. Here 
> is what came as a profile this time. 
> "http://i784.photobucket.com/albums/yy123/stefhoor/profile_y.jpg"
> Does this look "normal"? I am a bit worried since I have never worked 
> with this kind of calculation. The histogram looks fine, well spaced 
> overlaps between simulations.
> Thank you.

I would try to pull further than the distance you have.  It appears that the 
curve is only just starting to (maybe) level off.  You might have a look into 
the literature to see if anyone has done the same sort of thing on similar 
systems to get an idea of the total pull distance and the shape of the curve.


> ------------------------------------------------------------------------
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list