On 7/26/13 4:06 PM, Quintin Sheridan wrote:
Dear Gromacs Users,
Is it possible to run free energy calculations in parallel using mpirun? If
Yes, the free energy code is parallelized, either via MPI or threads.
not I am wondering what the fastest way to run a free energy calculation
is. I a
Dear Gromacs Users,
Is it possible to run free energy calculations in parallel using mpirun? If
not I am wondering what the fastest way to run a free energy calculation
is. I am basing my free energy calculation on the tutorial by Justin Lemkul
found at
http://www.bevanlab.biochem.vt.edu/Pages/Pe
On 6/21/13 11:07 AM, Dwey wrote:
Hi gmx-users,
I almost reproduced free energy calculations of methane in water on
Justin's website. First of all, I am able to follow the workflow of
computing solvation free energy for several times with Gromacs version
4.5.7 and version 4.6.2 install
Hi gmx-users,
I almost reproduced free energy calculations of methane in water on
Justin's website. First of all, I am able to follow the workflow of
computing solvation free energy for several times with Gromacs version
4.5.7 and version 4.6.2 installed in two identical Linux boxes.
Howe
Thank you Professor Shirts.
So now my protein itp file looks like this:
[ atoms ]
; nrtype resnr residue atom cgnr chargemasstypeB
chargeB MassB
1 CT1ACECH3 1 -0.190264 12.01 CT_per
-0.12033412.01
[ bonds ]
;ai aj func th0 kb th0
You have to change atom types. For example:
[ atomtypes ]
;name bond_typemasscharge ptype sigma epsilon
h1h1 0. 0. A 2.47135e-01 6.56888e-02
h1_pert h1 0. 0. A 2.47135e-01 3.56888e-02
; perturbed
The
Hi,
I am trying to perform expanded ensemble simulations between 2 states A
(lambda=0) and B (lambda =1) with 6 intermediate lambda values.
In state B the Hamiltonian is rescaled, such that the epsilons of the vdW
interactions, the charges, the bond, angle and dihedral constants are a
multiple of
--- On Fri, 2/11/12, Tom Kirchner wrote:
> Actually, this is a known problem. You should find the
> description and
> solution in the archive. I had the same problem, so this may
> make your
> search more easy :)
Thank you, it's good to know I'm not doing something wrong. Indeed, changing
298
Hi Fernandez,
Actually, this is a known problem. You should find the description and
solution in the archive. I had the same problem, so this may make your
search more easy :)
The problem is in the code, at some point float and numbers are messed
up, or something in this direction.
You can
Hi all,
Can I use the same simulations (with delta_lambda=0, init_lambda and
foreign_lambda) for TI and BAR calculations? I guess that boils down to whether
the simulations with foreign_lambda are in equilibrium with the init_lambda, or
they are some sort of hybrid ensemble between the differen
Ragothaman Yennamalli wrote:
Hi,
I want to run free energy calculations on a particular protein-ligand
complex. I do not have much knowledge on this so I have some questions,
hopefully someone might give me clear answers.
I am following the tutorial given in this link:
http://www.bevanlab.bi
Hi,
I want to run free energy calculations on a particular protein-ligand
complex. I do not have much knowledge on this so I have some questions,
hopefully someone might give me clear answers.
I am following the tutorial given in this link:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/g
eva.pluhar...@marge.uochb.cas.cz wrote:
Hi Justin,
thank you for suggestion about changing the integrator, but I would like
to know why it is not possible to sample properly by md under these
circumstances.
1. Do you know any papers about sampling efficiency of systems with almost
or complete
eva.pluhar...@marge.uochb.cas.cz wrote:
Hello all,
I am trying calculate desolvation free energy of Na+ in water using option
couple-moltype, not by creating B-topology in the .top file.
At first, I switched off coulombic interaction using:
couple-moltype = Na+
couple-lambda0
Hello all,
I am trying calculate desolvation free energy of Na+ in water using option
couple-moltype, not by creating B-topology in the .top file.
At first, I switched off coulombic interaction using:
couple-moltype = Na+
couple-lambda0 = vdw-q
couple-lambda1
Hi Ehud,
we recently developed an extended amber99sb forcefield + some scripts which
probably can do exactly what you want (setting up alchemical mutations for any
amino acid mutation except for proline).
We tested it by calculating thermostability differences for a set of 100+
mutations of an
I am investigating a certain peptide which is well bound to some
protein; their configuration is known from the PDB.
My aim is to compare the binding free energies of several variants of
the peptide.
In particular, I wish to mutate some amino acids to others.
I have read some tutorials and mail
Dear GROMACS users,
I am investigating a certain peptide which is well bound to some
protein; their configuration is known from the PDB.
My aim is to compare the binding free energies of several variants of
the peptide.
In particular, I wish to mutate some amino acids to others.
I have read
Dear All,
In my previous email the text in the message was not shown. Thats why I'm
writing this again.
I request to see the attachment of earlier message. I'm sorry for this!!
I have an disaccharide bound to a C-type lectin. The sequence of
disaccharide is beta-galactose1-4beta-GlcNAc. The 3
Dear All,
I have an disaccharide bound to a C-type lectin. The sequence of
disaccharide is beta-galactose1-4beta-GlcNAc. The 3'OH and 4'OH of
beta-galactose coordinate to the Ca2+ at the active site. FRET experiments
have shown that if the disaccharide linkage is changed to
beta-galactose1-3bet
Dear All,
I have a trimeric protein system which binds to two different ligands.
The ligands are oligosaccharides. The difference between the two is first
ligand has beta 1-4 linkage and the second ligand has beta 1-3 linkage
between Galactose (Gal) and N-Acetyl Glucosamine (GlcNAc). Since the l
Hello everybody
I tried to work with gromacs employing free energy calculations in a
dimeric protein system. First of all, doing a energy minimization a later
to compute the binding energy. For all the cases, I use amber 94 FF.
However, I have two questions.
1. When I made the energy minimizati
Hello all.
I worked with free energy calculations to obtain some information related
with solvation and binding free energy, analizing two proteins and using
amber94 force field. But, I have two questions.
1. When I tried to do a minization energy, I got the following message:
WARNING 1 [file
This looks like more of a pymbar question!
> I am trying to calculate free energy of a system that involves
> disappearance of LJ particle at lambda=1 in explicit solvent. I ran the
> simulation at 20 different lambda points ranging from 0 to 1, using soft
> core potential. In order to use MBAR m
Hi,
I am trying to calculate free energy of a system that involves
disappearance of LJ particle at lambda=1 in explicit solvent. I ran the
simulation at 20 different lambda points ranging from 0 to 1, using soft
core potential. In order to use MBAR method (python implementation from
Michael shirt
Can you be more specific in the question of what property you want to
compute for which molecule or molecules? Linear Interaction energy
approaches are not always very efficient for coulomb, and is
definitely not exact for the LJ term. So LIE might not be what you
want to be doing.
Michael Shirts
I'm interesting to calculate Gibbs energy using g_lie application.
Unfourtunately, I don't know what kind of state equation is the
sub-program using. Can you help me with that.
Best regards
Jorge R. Quintero
Grupo de Investigación en Fisicoquímica Teórica y Experimental
Universidad Industrial
Hi,
Note that there are proper options for this (no cut-off's):
ns_type = simple
pbc = none
nstlist = 0
rlist = 0
rcoulomb = 0
rvdw = 0
Berk.
> Date: Tue, 20 May 2008 12:45:35 -0700
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Free energy
Justin and Michael,
Just to clarify here, I don't think you want the "long cutoff in
vacuum" scheme to give you the same results as the "PME in vacuum"
scheme. That is, if you use PME in vacuum with a periodic box, you
will be including copies of the long-range unscreened electrostatic
interaction
Just to follow up - the cutoff scheme worked quite well. It gave me energies
that were ~1% different from those of the PME calculation, which I think
compares quite well. The 10-ps run I attempted now takes 3 seconds, instead of
20 minutes.
Thanks to everyone for the suggestions.
-Justin
Quot
Thanks to everyone for the insights. I'll try running things with the cutoff
and see how it goes.
-Justin
Quoting Michael Shirts <[EMAIL PROTECTED]>:
> Hi, Justin-
>
> Have you considered -not- running PME in vacuo? If you set your
> cutoffs and rlist large enough, then you can just run with
Hi, Justin-
Have you considered -not- running PME in vacuo? If you set your
cutoffs and rlist large enough, then you can just run with simple
cutoffs, and it should run -fst-. Of course, you should compare
to the energy with PME -- if they are not equivalent, then you many
need to go back an
ulate ridiculously long to reach
> the desired accuracy.
>
> Hope it helps,
> Jeroen
>
>
>
> Date: Mon, 19 May 2008 15:04:51 -0400
> From: "Justin A. Lemkul" <[EMAIL PROTECTED]>
> Subject: [gmx-users] Free energy calculations and speed problems
> To:
Lemkul" <[EMAIL PROTECTED]>
Subject: [gmx-users] Free energy calculations and speed problems
To: gmx-users@gromacs.org
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=ISO-8859-1
Hi all,
I'm running some free energy calculations (in vacuo and in solution)
Hi all,
I'm running some free energy calculations (in vacuo and in solution) for a set
of molecules I am trying to parameterize. All the molecules are fairly small,
about 30-35 atoms in each. The solvated calculations go smoothly, and rather
quickly (~5 hr/ns on two nodes). I am running into a
Quoting David Mobley <[EMAIL PROTECTED]>:
> Which gromacs version are you using?
Version 3.3.1 (forgot to mention that before, sorry!)
>
> I vaguely remember, that at one point I may have found a bug relating
> to atoms that initially started out with no charges and then had
> charges that were
Justin,
Following up on this, I looked back through my old e-mails and found
that, indeed, you do appear to be running into a known bug. It's one I
helped a guy named Bharat find, so the relevant bugzilla is from him
rather than from me: http://bugzilla.gromacs.org/show_bug.cgi?id=175.
It appears
Dear Justin,
> I'll preface this message by saying that this is my first foray into free
> energy
> calculations, and I am hoping that someone more well-versed in the matter may
> be
> able to help me sort out some strange results. I have done a good bit of
> reading in terms of tutorials and i
Hello all,
I'll preface this message by saying that this is my first foray into free energy
calculations, and I am hoping that someone more well-versed in the matter may be
able to help me sort out some strange results. I have done a good bit of
reading in terms of tutorials and in the archives,
difficult to sample.
But the capabilities of Gromacs are not the issue here.
Berk.
From: Maik Goette <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] free energy calculations in charged systems
Date: Wed, 21 N
Hi
Cant' give you a sound answer, but from what I heard from talking to
people in the field, PME can't handle that properly. Maybe
Cut-Off/Reaction-Field should be the long-range treatment of choice.
Still, I don't know, if there may occur problems with that.
Maybe David (both) or Berk have
Hi all,
i am working in polyelectrolyte solutions, and i would like to calculate the
free energy
for the polyectrolyte system (charged) to change to a neutral (non-charged)
system.
The question is if it feasible to use the PME electrostatics in gromacs for the
above
free-energy calculation.
Hi,
the review by David Pearlman can be very useful
in relation to FEP-type calculations
o Free Energy Calculations: Methods for Estimating
Ligand Binding Affinities
Chapter 2
In: Free energy calculations in
rational drug design
M. Rami Reddy & Mark D. Erion Eds.
Best regards,
Javier N.
Viswa
http://md.chem.rug.nl/education/Free-Energy_Course/index.html
http://www.dillgroup.ucsf.edu/~jchodera/group/wiki/index.php/Free_Energy:_Tutorial
Both very "decent".
Esther Caballero-Manrique
Guenza Group
University of Oregon
Eugene, OR (USA)
Viswanadham Sridhara wrote:
Hello gmx-users,
I wa
Hello gmx-users,I wanted to know whether there are any tutorials available on free energy calculations with Gromacs.I have done some survey, but was curious to find out any "decent" tutorials available.
Thanks in advance,-Vissu.-- Viswanadham Sridhara,Research Assistant,Old Dominion University,Norf
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