Re: [gmx-users] Sampling windows

Hi Xavier Thanks very much for your time. That has mad things very clear Gavin Avier Periole wrote: > > On Jan 5, 2011, at 6:03 PM, Gavin Melaugh wrote: > >> Hi Xavier >> >> Many thanks. Two more quick questions (both refering to barrier region): >> Does the value of the force constant affect th

Re: [gmx-users] Sampling windows

On Jan 5, 2011, at 6:03 PM, Gavin Melaugh wrote: Hi Xavier Many thanks. Two more quick questions (both refering to barrier region): Does the value of the force constant affect the height of the barrier providing that there is reasonable overlap? No! The force constant used does not affect t

Re: [gmx-users] Sampling windows

Hi Xavier Many thanks. Two more quick questions (both refering to barrier region): Does the value of the force constant affect the height of the barrier providing that there is reasonable overlap? Obviously there is a compromise between the size of the constant and the number of windows. If I incr

Re: [gmx-users] Sampling windows

On Jan 5, 2011, at 5:01 PM, Gavin Melaugh wrote: Hi Xavier Many thanks for the reply. When I compare the two curves Curve 1) lack of overlap in barrier region; force constant = 1000 Curve 2) with increased number of sampling windows with increased force constant (note I have only increased

Re: [gmx-users] Sampling windows

Hi Xavier Many thanks for the reply. When I compare the two curves Curve 1) lack of overlap in barrier region; force constant = 1000 Curve 2) with increased number of sampling windows with increased force constant (note I have only increased the force constant of the windows in the barrier region)

Re: [gmx-users] Sampling windows

On Jan 5, 2011, at 4:08 PM, Gavin Melaugh wrote: Dear all I have generated a PMF curve for introducing a guest molecule into a host molecule using the umbrella sampling method. The curve seems fine, but there are no overlaps between histograms in the barrier region. To circumvent this I hav