Thanks Berk,
What you're saying makes perfect sense. I should be using one 2D bias
instead of two 1D biases. And I should use a cutoff on the free energy.
This way gmx awh should generate a 2D PMF. So far I've only modified my
.mdp file like this to have one 2D bias, but haven't put the free energy
cutoff yet (not sure what a sensible value would be).
pull = yes
pull_ngroups = 3
pull_ncoords = 2
pull-group1-name = TYS14
pull-group2-name = TOX_SURFACE
pull-group3-name = TYS3
pull-coord1-groups = 1 2
pull-coord1-type = external-potential
pull-coord1-potential-provider = AWH
pull-coord1-geometry = distance
pull-coord2-groups = 1 3
pull-coord2-type = external-potential
pull-coord2-potential-provider = AWH
pull-coord2-geometry = distance
;
awh = yes
awh-nstout = 10000
awh-nbias = 1
awh1-ndim = 2
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
awh1-dim2-coord-index = 2
awh1-dim2-start = 0.3
awh1-dim2-end = 3.8
awh1-dim2-diffusion = 1.0e-6
awh1-dim2-force-constant = 1000000
However something very strange is happening with my job when I try to
run it on the server. The simulation seems to run very slow, doesn't
manage to use the GPUs at all, doesn't use the CPUs properly either and
is using more than 95% of the machine's memory (normally it uses about
0.5%). Importantly, it also generates huge energy and checkpoint files
within half-an-hour. I've killed the previous job and started again but
it's doing the same thing.
-bash-4.2$ ll -trh
total 21G
drwxr-xr-x. 2 cleyrat granier 4.0K Feb 14 19:53 restraints
drwxr-xr-x. 2 cleyrat granier 4.0K Feb 14 19:53 toppar
-rw-r--r--. 1 cleyrat granier 5.3M Feb 14 19:54 index_awh.ndx
-rw-r--r--. 1 cleyrat granier 12M Feb 14 19:56 step6.6_equilibration.gro
-rw-r--r--. 1 cleyrat granier 2.3K Feb 14 19:56 step7_production2_awh1.mdp
-rw-r--r--. 1 cleyrat granier 2.2K Feb 14 19:56 step7_production2_awh4.mdp
-rw-r--r--. 1 cleyrat granier 1.6K Feb 14 19:56 topol.top
-rw-r--r--. 1 cleyrat granier 8.2M Feb 14 19:57 step7_awh4.tpr
-rw-r--r--. 1 cleyrat granier 5.9M Feb 14 20:08 step7_awh4.trr
-rw-r--r--. 1 cleyrat granier 4.9M Feb 14 20:19 step7_awh4.xtc
-rw-r--r--. 1 cleyrat granier 2.2K Feb 14 20:19 step7_production2_awh5.mdp
-rw-r--r--. 1 cleyrat granier 9.0G Feb 14 20:21 step7_awh4.cpt
-rw-r--r--. 1 cleyrat granier 1.7G Feb 14 20:21 step7_awh4.edr
-rw-r--r--. 1 cleyrat granier 36K Feb 14 20:21 pullx_step7_awh4.xvg
-rw-r--r--. 1 cleyrat granier 43K Feb 14 20:21 pullf_step7_awh4.xvg
-rw-r--r--. 1 cleyrat granier 83K Feb 14 20:21 step7_awh4.log
-rw-r--r--. 1 cleyrat granier 16K Feb 14 20:23 mdout.mdp
-rw-r--r--. 1 cleyrat granier 8.2M Feb 14 20:23 step7_awh5.tpr
-rw-r--r--. 1 cleyrat granier 5.9M Feb 14 20:35 step7_awh5.trr
-rw-------. 1 cleyrat granier 7.5K Feb 14 20:41 nohup.out
-rw-r--r--. 1 cleyrat granier 6.1M Feb 14 20:49 step7_awh5.xtc
-rw-r--r--. 1 cleyrat granier 2.2G Feb 14 20:50 step7_awh5.edr
-rw-r--r--. 1 cleyrat granier 90K Feb 14 20:50 step7_awh5.log
-rw-r--r--. 1 cleyrat granier 47K Feb 14 20:50 pullx_step7_awh5.xvg
-rw-r--r--. 1 cleyrat granier 55K Feb 14 20:50 pullf_step7_awh5.xvg
-rw-r--r--. 1 cleyrat granier 7.5G Feb 14 20:51 step7_awh5_step96200.cpt
-bash-4.2$
Is this some kind of bug or am I doing something wrong with the parameters?
Cedric
Le 2/14/2019 à 8:09 PM, Berk Hess a écrit :
Note though, as also noted in the manual, you need to be careful what you wish
for. 2D biasing leads to uniform sampling of the requested rectangular area.
Often you want to suppress sampling of high free-energy (unphysical or
uninteresting) regions in this rectangle by using a cutoff on the free-energy.
________________________________
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Berk Hess
<g...@hotmail.com>
Sent: Thursday, February 14, 2019 5:41 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] AWH with two bias potentials
I see now that you used awh-nbias=2 with awh-ndim=1. Thus you asked for 2
independent 1D AWH biases and PMFs. You might be able to get a 2D PMF from
that, but that is complicated.
I think that what you want is one 2D bias: awh-nbias=1 with awh-ndim=2.
Berk
________________________________
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Cédric Leyrat
<cedric.ley...@igf.cnrs.fr>
Sent: Thursday, February 14, 2019 4:32 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] AWH with two bias potentials
Dear Berk,
I do get a set of PMF files at different times for each reaction
coordinate from gmx awh. Each file has two columns (x=coordinate 1,
y=PMF or x=coordinate 2, y=PMF). My coding and maths skills are quite
limited so if you have a script that can convert these data to a 2D
format, I would be happy to use it.
Cedric
Le 2/14/2019 à 3:27 PM, Berk Hess a écrit :
gmx awh writes out the 2D (or any-D) PMF to xvg files for different times. The
1D nature of xvg files is not convenient for visualization though, so you need
to write a script to convert it to you favorite 2D data format. I probably have
a script somewhere for some 2D format (python?) if you can't write it yourself.
Berk
--
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<http://www.researchgate.net/profile/Cedric_Leyrat<http://www.researchgate.net/profile/Cedric_Leyrat<http://www.researchgate.net/profile/Cedric_Leyrat>>
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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
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