On Fri, May 18, 2012 at 12:22 PM, Justin A. Lemkul <[email protected]> wrote:
> > I have no idea why you observe the dip, but it's probably irrelevant as > you don't need a reaction coordinate that long, if this is the same plot > that we've been discussing on the list. > > I must ask that you always post to the mailing list, for your own benefit, > especially in the immediate future as I will be traveling for some time and > will not reply very quickly to email; you stand a better chance getting > help from others. I am also generally unable to dedicate much time > debugging others' research on a personal level. > > -Justin > > Thank you Justin. I decreased the reaction coordinate and this dip still occurs: http://speedy.sh/2qHNa/Profile2.JPG Its because of the applied weight of WHAM. Any suggestions please? Steven > > On 5/18/12 4:17 AM, Steven Neumann wrote: > >> Dear Justin, >> >> >> I run umbrella sampling (pulling ligand away from the protein) >> simulations to >> get deltaG: >> >> http://speedy.sh/XpUks/**Profile.JPG <http://speedy.sh/XpUks/Profile.JPG> >> >> http://speedy.sh/yvJKx/**Histogram.JPG<http://speedy.sh/yvJKx/Histogram.JPG> >> >> I know I need one more window around 1 nm but apart from this histrogram >> looks >> really good. My each window was 50 ns. >> >> Why the plateau in the end goes down of 0.4 kcal/mol? Would you suggest >> longer >> simulation in each window? >> >> Thank you and sorry for writing straight to your email, >> >> Best >> >> Steven >> >> >> > -- > ==============================**========== > > 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== >
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