[gmx-users] Poor sampling in PMF at some points

Christopher Neale chris.neale at alum.utoronto.ca
Sun Nov 27 17:57:14 CET 2016

Most likely is that you have a very unfavorable position there. If so, the solution would be to add some umbrellas in that range that employ stronger force constants. However, before you do that, maybe try to run wham again with a larger bin width (large as you need to get an output PMF) and see if there is a local maxima there. You could also use gmx distance or gmx traj or some other tool to evaluate your actual sampling to (a) see if you did get any sampling in that region and (b) if not, to identify frames near the boundary so that you can view them in VMD and see why they might not have entered this region.

From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Alex <alexanderwien2k at gmail.com>
Sent: 27 November 2016 10:47:40
To: gmx-users at gromacs.org
Subject: [gmx-users] Poor sampling in PMF at some points

Dear gromacs user,

In my PMF calculation by umbrella sampling in z direction, I have surely
considered some windows or configuration in

z= "... 1.878, 1.886,  1.891, 1.902, 1.911, 1.932, 1.949, 1.959, 1.961

but I do not know why I have poor sampling in the some point which are
really close to the above points which I had considered configuration for

for example :
WARNING, no data point in bin 22 (z=1.89414)

WARNING, no data point in bin 23 (z=1.91285)

WARNING, no data point in bin 24 (z=1.93156)

WARNING, no data point in bin 25 (z=1.95026)

WARNING, no data point in bin 26 (z=1.96897)

Here is my pull part of mdp file which run for 30 ns for each windows:
pull                     = yes
pull-ngroups             = 2
pull-ncoords             = 1
pull-group1-name         = Protein
pull-group2-name         = Other

pull-coord1-groups       = 1 2
pull-coord1-type         = umbrella
pull-coord1-dim          = N N Y
pull-coord1-start        = yes
pull-coord1-rate         = 0.0
pull-coord1-geometry     = distance
pull-coord1-k            = 1500   ;;kJ/(mol nm^2)
pull-print-components    = Yes
pull-nstxout             = 1000
pull-nstfout             = 1000
pull-print-com1          = yes


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