Re: [gmx-users] Umbrella sampling - regd

2013-01-01 Thread ramesh cheerla
Dear Justin, Thank you very much for your quick reply. Regards, Ramesh. On Wed, Jan 2, 2013 at 10:24 AM, Justin Lemkul wrote: > > > On 1/1/13 11:48 PM, ramesh cheerla wrote: > >> Dear Gromacs users, >> >> I am performing umbrella samplin

Re: [gmx-users] Umbrella sampling - regd

2013-01-01 Thread Justin Lemkul
On 1/1/13 11:48 PM, ramesh cheerla wrote: Dear Gromacs users, I am performing umbrella sampling simulations by selecting configurations with spacing window of 0.02nm from pulling simulations with the following options in .mdp file to get PMF along a axis

Re: [gmx-users] Umbrella sampling - regd

2012-11-26 Thread ramesh cheerla
Dear Justin, I am very thankful to you for your reply, you are correct, I have plotted the histo.xvg file in wrong manner. After plotting histograms in correct manner I have realized that my sampling is very poor as histograms and there overlapping is restricted to some regions only, no histogram

Re: [gmx-users] Umbrella sampling - regd

2012-11-26 Thread Justin Lemkul
On 11/26/12 1:03 AM, ramesh cheerla wrote: Dear Gromacs users, I am calculating PMF for the ion permeation through a tunnel, using umbrella sampling. In my system I have some binding sites with ions, I have removed some ions from binding sites before pulling and In pulling simulations