Emanuel Birru wrote:
I have tried the free energy calculation using 4.5.3, but when I run
g_bar it still gives me the following and do not generate the output
files.
prod.xvg: 0.0 - 5000.0; lambda = 0.000
foreign lambdas: 0.000 (125001 pts) 0.000 (125001 pts) 0.010 (125001
pts) 0.030 (125001 pts) 0.050 (125001 pts) 0.100 (125001 pts) 0.200
(125001 pts) 0.300 (125001 pts) 0.400 (125001 pts) 0.500 (125001 pts)
0.600 (125001 pts) 0.650 (125001 pts) 0.700 (125001 pts) 0.750 (125001
pts) 0.800 (125001 pts) 0.850 (125001 pts) 0.900 (125001 pts) 0.950
(125001 pts) 1.000 (125001 pts)
No results to calculate.
I put my mdp file for production run and the output file prod.xvg on
the following links for your consideration.
http://hydra.pharm.monash.edu.au/md_project/production.txt (mdp file)
http://hydra.pharm.monash.edu.au/md_project/prod.txt (xvg file)
From the above g_bar output and the .xvg file, it seems that lambda=0 is
considered both native and foreign, which probably causes the algorithm to fail.
Note, too, that the results in the first column of the .xvg file (which would
correspond to some weird difference between lambda=0 and lambda=0, which should
not exist!) also seem to be nonsensically high. This is what I mean when I say
weird results from simultaneous (de)coupling of charges and LJ terms. The
systems are not completely stable, yielding weird energies. The result could
also be some bizarre result of lambda=0 being considered native and foreign.
Based on the .mdp file, I don't know how this could have happened, but all signs
point to some sort of problem with the input.
-Justin
Cheers,
Emanuel
-----Original Message-----
From: [email protected]
[mailto:[email protected]] On Behalf Of Justin A. Lemkul
Sent: Thursday, 24 March 2011 2:02 PM
To: Gromacs Users' List
Subject: Re: [gmx-users] no output dgdl file
Emanuel Birru wrote:
Yeah, I am using IT and do analyse the result using another method not
bar. But I used g_bar when I was using the foreign_lambda and simulate
all in a single file. I have already sent my suspect few weeks back.
Is there an active redmine issue? I cannot find any post from you in
the list
archive from the last few months. What is the issue?
I am a bit confused on the g_bar part, when it says -f expects
multiple
dhdl files. Do we need to run still multiple independent simulations
using different foreign_lambda values? I do not see why we should run
independent simulations, if we use for couple-lambda0 and
couple-lambda1
vdw-q and none respectively.
As I mentioned to the OP of this thread, simultaneous (de)coupling of
vdW and
Coulombic interactions is not stable. The output energies are not
trustworthy,
in my experience due to physically unreasonable configurations and the
potential
for numerical singularities.
The multiple files that g_bar expects are not simply from two separate
processes, however. It expects dhdl.xvg files from multiple values of
native
lambda that have corresponding foreign_lambda values in it, i.e.:
Interval 1:
init_lambda = 0
foreign_lambda = 0.05
Interval 2:
init_lambda = 0.05
foreign_lambda = 0 0.1
Interval 3:
init_lambda = 0.1
foreign_lambda = 0.05 0.15
etc.
-Justin
For IT I am using 4.5.3 and it is working good so far.
Cheers,
-----Original Message-----
From: [email protected]
[mailto:[email protected]] On Behalf Of Justin A. Lemkul
Sent: Thursday, 24 March 2011 1:36 PM
To: Gromacs Users' List
Subject: Re: [gmx-users] no output dgdl file
Emanuel Birru wrote:
Hi Justin,
It good that the issue is solved. As per my experience if you want to
do
a series of simulations it is not necessary to use foreign_lambda,
for
each simulation we can give different lambda values starting from 0
to
1( from fully interactive to non-interactive) no need of
foreign_lamda
This is certainly a viable method, but it is thermodynamic
integration,
not BAR.
The purpose of lambda/foreign_lambda is to use the BAR method.
and certainly no need of generating dhdl.xvg to calculate FE. I think
-dhdl is an optional it will not be generated just because
"free_energy
= yes" is present. The problem with the 4.5.3 is not the problem of
It has always been my experience (in versions 3.3.3 and 4.5.3) that if
the free
energy code is activated, this file is written. I never specify the
file names
independently.
generating dhdl data by using single simulation with all
foreign_lambda
values. The problem is with g_bar, when I tried to analyse the
dhdl.xvg
output (with all the necessary data in it) using g_bar, it doesn't
function properly. The error is related with the source code. I guess
If you suspect a bug, you should report it. If you don't use
foreign_lambda,
you can't use the BAR method. You're doing TI, not BAR. They are
fundamentally
different, and the analysis for TI is done independently of any
Gromacs
tool.
the main advantage of using 4.5.3 to calculated FE using
foreign_lambda
was to avoid running series of independent simulations. May be it is
solved on the newer version 4.5.4., didn't try it yet.
Version 4.5.3 has worked just fine for all free energy calculations I
have done.
Perhaps BAR can be done with a single simulation and multiple
foreign_lambda,
but that was not my understanding of the proper procedure (based on
some
posts
by developers a few months ago). Multiple simulations, each at
"native"
lambda,
are conducted with values of foreign_lambda above and below the native
value at
some lambda spacing (except for end points). Invoking g_bar gives the
total
DeltaG over all lambda intervals according to the BAR algorithm.
-Justin
Cheers,
-----Original Message-----
From: [email protected]
[mailto:[email protected]] On Behalf Of Justin A. Lemkul
Sent: Thursday, 24 March 2011 12:54 PM
To: Gromacs Users' List
Subject: Re: [gmx-users] no output dgdl file
Emanuel Birru wrote:
Hi Justin,
Sure what you wrote is correct, what I am trying to tell to him is
that
if he has more than one foreign lambda it is better to put all of
them
as it is not logical to use only one foreign lambda to calculate FE
(0
-
0.1) and he doesn't have delta lambda too. -Deffnm is sure all about
You can do a series of simulations at many values of lambda, each
specifying
their own foreign_lambda. It seems to me that this method would be
more
reliable, but I have not tested simply attempting a single simulation
with all
values of foreign_lambda. Using delta_lambda is (from all that I
have
read) not
reliable, as there are known issues with "slow growth" methods.
file names but it also generate all the necessary files including
the
xvg's without the need of using -dhdl.
Whether or not one specifies -dhdl or -deffnm is independent of
whether
or not
dhdl.xvg (or whatever name) is written. It is controlled purely by
the
presence
of "free_energy = yes" in the input file.
I would appreciate if you come up with a new solution for him.
As reported by the OP, this issue had been effectively solved
already:
http://lists.gromacs.org/pipermail/gmx-users/2011-March/059631.html
-Justin
Cheers
-----Original Message-----
From: [email protected]
[mailto:[email protected]] On Behalf Of Justin A. Lemkul
Sent: Thursday, 24 March 2011 12:35 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] no output dgdl file
Emanuel Birru wrote:
Hi,
Your foreign_lambda value is only one, please put all your lambda
values
separated by space and you will get the dhdl file. And make sure
that
This is not required. You can specify as many or as few
foreign_lambda
values
as you like.
you use -deffnm when you run your mdrun to get all the out put
files
by
default.
The -deffnm flag controls the names of the files, not which ones are
written.
-Justin
Cheers,
*From:* [email protected]
[mailto:[email protected]] *On Behalf Of *Moeed
*Sent:* Thursday, 24 March 2011 4:13 AM
*To:* [email protected]
*Subject:* [gmx-users] no output dgdl file
Hello,
I have a little problem with FE output file. Below is the settings
and
also I am including -dgdl in the command I issue but no dgdl (or
dhdl)
file generates. I dont figure where the problem lies ! (version
4.5.3).
free_energy = yes
init_lambda = 0
delta_lambda = 0
sc_alpha = 0.5
sc-power = 1
sc_sigma = 0.3
foreign_lambda = 0.1
dhdl_derivatives = yes
couple-moltype = Polymer
couple-lambda0 = vdw-q
couple-lambda1 = none
couple-intramol = yes
nstdhdl = 10
separate_dhdl_file = yes
dh_hist_size = 0
dh_hist_spacing = 0.1
Best
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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