[gmx-users] Umbrella Sampling - good histogram but no result in profile

[Ben Tam]

Hi Neha,

I have tried that, I have reduced the number of reaction coordinate (from 42 to 10 windows) and still it gives me "nan". I have check each specific pullf.xvg and pullx.xvg, there are non zero value inside. Hence forth I don't understand what else going on.

Hi Mark,

Okay I will do that. However what file should I need to attach with the issue?

Thank you both for your answer. However I have one more question. When using gmx wham, it is either pullf.dat or pullx.dat are need to provide. As far as I know, you need the force act upon the position of the molecules. What I don't understand is, why do I only need to provide pullx or pullf but not both? how does "gmx wham" understand at what position that the force is applied or vice versa?  is it because it read it off .tpr?

Thank you very much,

Ben
________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Awasthi, Neha <neha.awasthi at biologie.uni-goettingen.de>
Sent: Wednesday, March 14, 2018 15:16
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Umbrella Sampling - good histogram but no result in profile

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

Hi,

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.

Mark

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,
> direction-periodic
> 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,
>
> Ben
>
>
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