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.
Cedric
--
Cédric LEYRAT, Ph.D
Chargé de recherche - INSERM
PHARMACOLOGY AND STRUCTURAL BIOLOGY OF MEMBRANE PROTEINS
Institut de Génomique Fonctionnelle
U1191 INSERM
141, rue de la cardonille
34094 Montpellier Cedex 05 - France
tel: +33 (0)434359272
www.researchgate.net/profile/Cedric_Leyrat
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
