[gmx-users] gmx wham problem

[Thompson, Matthew White]

It looks like you need to sample more states, 13 is not enough. Probably more like 20-30+ would be needed to get a smooth PMF as is discussed in that tutorial. The weird features in your PMF are from insufficiently overlapping histograms, for example the bump near -2.2 nm corresponds to having no histogram there. You also see that you only have one state near -1.2 nm, so that is probably not being sampled enough for WHAM to produce meaningful results.

Also I don't understand the meaning of negative distance as a reaction coordinate. If that is the distance between two things, maybe it should be positive. It makes it difficult to understand which values correspond to them being close and far away.
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From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of edesantis [edesantis at roma2.infn.it]
Sent: Wednesday, June 28, 2017 10:26 AM
To: Gmx users
Subject: [gmx-users] gmx wham problem

dear all,

I am studying the affinity between an antibody and an amyloid peptide; I
am interested in the evaluation of the PMF. I have a problem with the
PFM shape.
I followed the protocol described in the umbrella-sampling tutorial
(http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/01_pdb2gmx.html)
Here below there is the .mdp part for the pulling
; Pull code
pull                    = yes
pull_ngroups            = 2
pull_ncoords            = 1
pull_group1_name        = Chain_Abeta
pull_group2_name        = Chains_Antibody
pull_coord1_type        = umbrella      ; harmonic biasing force
pull_coord1_geometry    = direction
pull_coord1_groups      = 1 2
pull_coord1_vec         =  38.207 68.611 29.8493
pull_coord1_rate        = 0.002        ; 0.01 nm per ps = 10 nm per ns
pull_coord1_k           = 1000          ; kJ mol^-1 nm^-2
pull_coord1_start       = yes           ; define initial COM distance >
0

After the pulling simulation, I’ve extracted 13 configuration; for each
them, 36 ns of equilibration were performed. These are the mdp
directives:
; Pull code
pull                    = yes
pull_ngroups            = 2
pull_ncoords            = 1
pull_group1_name        = Chain_Abeta
pull_group2_name        = Chains_Antibody
pull_coord1_type        = umbrella      ; harmonic biasing force
pull_coord1_geometry    = direction
pull_coord1_groups      = 1 2
pull_coord1_vec         = 38.207 68.611 29.8493
pull_coord1_rate        = 0.00
pull_coord1_k           = 1000          ; kJ mol^-1 nm^-2
pull_coord1_start       = yes           ; define initial COM distance >
0

Then I ran the wham command:
Gmx wham –it list_tpr.dat –if list_pullf.dat -v  –b 20000 –o –hist
And I’ve obtained the following pictures:
http://i66.tinypic.com/11t5zdv.png
http://i67.tinypic.com/30u8g8x.png
Do you have any idea of why the pfm profile has this strange shape?
Could it come from any kind of error I’ve made during the simulations?
If there are not errors, it seems that the configurations in which the
peptide is far from the antibody are more energetically favoured respect
to those in contact with the antibody, but I have some doubts about it…

Can you help me?
Thank you in advance,
best regards,
Emiliano


--
Emiliano De Santis
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