[gmx-users] Umbrella Sampling - good histogram but no result in profile
neha.awasthi at biologie.uni-goettingen.de
Wed Mar 14 16:16:18 CET 2018
Before labeling this as a bug and reporting on redmine, I suggest you try :
1) calculate the profile over part(s) of your reaction coordinate, i.e. reduce the number of windows you work with.
In other words, start with small number of windows in pullx-files.dat & tpr-files.dat.
If you get partial profiles, it would point towards some windows (along your reaction coordinate) that cause problems. One needs to patiently test increasing number of windows.
2) A small region of poor overlap can lead to profiles with nan.
high k value should not be a problem provided you have the required number of windows and the histograms overlap (check about how much overlap is good overlap) . Sometimes, along a steep profile, histograms are difficult to assign, and tend to shift leading to small regions of poor overlap.
Hope this helps.
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Mark Abraham <mark.j.abraham at gmail.com>
Sent: Wednesday, March 14, 2018 3:51 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Umbrella Sampling - good histogram but no result in profile
That would generally suggest something divided by zero, or similar, eg
because no data was in a histogram bin, etc.
That behavior is a bug that we could perhaps fix if you would be so kind as
to report it at https://redmine.gromacs.org.
But the core problem remains that something about how you sampled didn't
meet the expectations of gmx wham.
On Wed, Mar 14, 2018, 15:45 Ben Tam <btam125 at hotmail.co.uk> wrote:
> Dear all,
> I have a rather strange problem. Currently I am trying to get a PMF of a
> water molecule through a hydrophobic materials. At the end of using "gmx
> wham", I get a rather good histogram and it cover the whole range of the
> system. However at the making profile.xvg. I get the answer "nan" inside
> the file. Therefore I really cannot think of why is it giving me that?
> Currently I set it as :
> ;Pull code
> pull = yes
> ;pull-cylinder-r = 0.5
> pull_ngroups = 2
> pull_ncoords = 1
> pull_group1_name = SOL
> pull_group2_name = MOL
> pull_coord1_type = umbrella ; harmonic biasing force
> pull_coord1_geometry = direction-periodic ; simple distance increase,
> pull_coord1_vec = 1 1 1
> pull_coord1_groups = 1 2
> pull_coord1_dim = Y Y Y
> pull_coord1_rate = 0.00 ; 0.01 nm per ps = 10 nm per ns
> pull_coord1_k = 10000 ; kJ mol^-1 nm^-2
> pull_coord1_start = yes ; define initial COM distance > 0
> Also this appears when I used the command "gmx wham":
> Switched to exact iteration in iteration 1
> 1) Maximum change -1.000000e+20
> Converged in 2 iterations. Final maximum change -1e+20
> Therefore I really don't understand what I have to do in order to get a
> profile.xvg. I understand the k value is high, but without that high value,
> the water won't settle within the assign window.
> Am I doing something wrong? because I got a good histogram but no result
> in the profile.xvg? Thank you very much for your help.
> Best regards,
> Gromacs Users mailing list
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