[gmx-users] Umbrella_pull_simulation

Justin A. Lemkul jalemkul at vt.edu
Mon Feb 20 15:54:48 CET 2012

shahid nayeem wrote:
> Thanks Justin
> I have pulled one of the chain from an initial COM distance value of 
> 3.65 A to 7.90 A. When I look this trajectory in VMD I find that the 

I will have to assume you mean nm.  Gromacs does not deal in Angstrom, and these 
distances would be within any sensible short-range cutoff and thus not 
indicative of actual separation.

> chain is completely separated. But even at this separation the 
> profile.xvg file does not show its convergence to one value. I sent this 
> file to you earlier.

Sorry, I don't have a photographic memory, nor can I recall if you've ever 
posted your .mdp file, or at the very least, told us how much sampling you've 
done in each window.  It may well be that your simulations are simply too short 
to observe adequate post-equilibration sampling.



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