[gmx-users] AWH with two bias potentials

Cédric Leyrat Cedric.Leyrat at igf.cnrs.fr
Thu Feb 14 15:02:50 CET 2019

Dear Gromacs users,

I'm simulating a system composed of a transmembrane receptor interacting 
with a 30 kDa soluble protein that sits on top of it. The receptor has a 
~ 20 residue tail that is supposed to interact with the soluble protein. 
I'm trying to predict the most stable conformation of this tail onto the 
soluble protein surface. In order to do this, I've been trying to use 
the accelerated weight histogram (AWH) method. I'm applying two 
independent biases. One is the COM distance between the receptor tail 
and a group of residues at the surface of the soluble protein, and the 
other is the distance between two residues that are part of the tail. My 
.mdp file looks like this:

pull                    = yes
pull_ngroups            = 4
pull_ncoords            = 2
pull-group1-name        = TYS14
pull-group2-name        = TOX_SURFACE
pull-group3-name        = TYS3
pull-group4-name        = TYS14
pull-coord1-groups      = 1 2
pull-coord1-type        = external-potential
pull-coord1-potential-provider = AWH
pull-coord1-geometry    = distance
pull-coord2-groups      = 3 4
pull-coord2-type        = external-potential
pull-coord2-potential-provider = AWH
pull-coord2-geometry    = distance
awh                     = yes
awh-nstout              = 10000
awh-nbias               = 2
awh1-ndim               = 1
awh1-dim1-coord-index   = 1
awh1-dim1-start         = 0.001
awh1-dim1-end           = 3.8
awh1-dim1-diffusion     = 1.0e-6
awh1-error-init         = 10000.0
awh1-dim1-force-constant = 1000000
awh2-ndim               = 1
awh2-dim1-coord-index   = 2
awh2-dim1-start         = 0.3
awh2-dim1-end           = 3.8
awh2-dim1-diffusion     = 1.0e-6
awh2-error-init         = 10000.0
awh2-dim1-force-constant = 1000000

Although I was not too sure how to setup the AWH parameters, the 
simulation seems to be running fine (the tail is moving fast and 
sampling a whole bunch of states). The two pull coordinates are being 
written to pullx.xvg and gmx awh can output the PMF for each bias. My 
question is: is it possible to calculate the two-dimensional PMF or FEL 
(maybe using gromacs tools like sham or wham?) and how to do it?
I haven't been able to find any practical information about that in the 
manual, in the gmx_users archives or in Viveca Lindahl's papers.
If someone could explain me how to do this that would be really nice.


Cédric LEYRAT, Ph.D
Chargé de recherche - INSERM
Institut de Génomique Fonctionnelle
141, rue de la cardonille
34094 Montpellier Cedex 05 - France
tel: +33 (0)434359272

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