Dear Gmx Users,
I wish to compare binding free energy obtained from US which I have
sucsessfully conducted and the one obtained using FEP. Would you suggest
any tutorial?
Steven
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please
Hi all!
I have a problem. So as it can be seen in the theme I am trying to improve
sampling of free energy calculating simulation by using replica exchange.
In the gmx4.6 it is simple while using FEP technique, but does not
implemented for umbrella sampling. But I want evaluate potential of mean
Hi Fabian,
I am trying something similar with Glutamate to Alanine mutation.
Does your dummy atoms i.e., DUM1 have a value of 0.0 for sigma and epsilon
during all three steps or only in step 2?
Thanks for the time,
Sai
On Thu, Apr 26, 2012 at 10:43 AM, Fabian Casteblanco
Hello all,
This is in reply to Michael shirts a while ago on a FEP of a R-CH3 to
an R-H group. Below is the orignal email. I recently tested out
mutating a CH3-CH3-(3dummy atoms) molecule on both sides in order to
test out that a peturbation would give you a total of 0. forcefield
used was
Hi,
Is it possible in GROMACS4.5 to perform computation of relative binding free
energy of a ligand to a protein due to mutation in the ligand ( or due tio
mutation in the protein)?
I have done the computation of solvation free energy of a solute in a solvent
using FEP but looking for some
On 23/01/2012 7:06 AM, Sanku M wrote:
Hi,
Is it possible in GROMACS4.5 to perform computation of relative
binding free energy of a ligand to a protein due to mutation in the
ligand ( or due tio mutation in the protein)?
I have done the computation of solvation free energy of a solute in a
Dear all,
I'm trying to FEP away a TIP4P water molecule from a water box in gmx
4.5.3, but getting a jump in dH/dlambda after some time (around 100 ps),
from around -5 to -600 kJ/mol/lambda. I'm using softcore with the
following parameters:
sc-alpha = 0.5
sc-power = 1
sc-sigma = 0.3
Hi Gmx Users,
Can you suggest some reading and some tutorial in calculations of binding
free energy (ligand binding) in Gromacs? ?I want to use Free Energy
Perturbation method.
Steven
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please
Hi
Please have a look at Dr.Justin tutorial page at the following link:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html
Cheers
On Mon, Oct 10, 2011 at 12:27 PM, Steven Neumann s.neuman...@gmail.comwrote:
Hi Gmx Users,
Can you suggest some reading and some
Hi Gmx Users,
Can you suggest some reading and some tutorial in calculations of binding
free energy (ligand binding) in Gromacs? ?I want to use Free Energy
Perturbation method.
Steven
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please
mohsen ramezanpour wrote:
Hi
Please have a look at Dr.Justin tutorial page at the following link:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html
This tutorial is not for FEP explicitly, but may be of some use. There is
discussion on using the BAR
Thank you guys! So, is there any tutorial in Gromacs for calculating free
energy of ligand binding using FEP?
Steven
On Mon, Oct 10, 2011 at 2:02 PM, Justin A. Lemkul jalem...@vt.edu wrote:
mohsen ramezanpour wrote:
Hi
Please have a look at Dr.Justin tutorial page at the following link:
Steven Neumann wrote:
Thank you guys! So, is there any tutorial in Gromacs for calculating
free energy of ligand binding using FEP?
TI or BAR are better methods for calculating binding free energies, I would
think. FEP is best for mutating between different species.
-Justin
Steven
FEP is a poorly defined term. It can either mean 1) making small
changes 'alchemical' changes in the molecules and computing the free
energies by any method (BAR, TI, etc), or 2) it can mean specifically
computing the free energies by exponentially averaging the potential
energy differences.
Hi all,
I have an additional question related to what Steven Neumann was
mentioning. I actually have to do a molecule mutation. I'm trying to
use Michael Shirts method 1) making small
changes 'alchemical' changes in the molecules and computing the free
energies by any method (BAR, TI, etc).
So BAR is only
referring to the mathematical code used to calculate the overall free
energy for the FEP, correct?
Yes. The information required is the same, with the exception that
exponential averaging requires energy differences from only one state,
whereas BAR requires energy differences
This is a tough issue and there are some unresolved questions here.
I recommend seeing the work of Kastenholz and Hunenberger on ion solvation
in JCP a couple years ago (two companion papers) as these explain the key
issues.
Thanks.
On Wed, Aug 17, 2011 at 3:24 AM, Marcelino Arciniega Castro
Hi there,
Could someone please share some ideas about the next situation?:
I am trying to estimate the relative binding affinity of two small molecules to
a protein. In the setup process, ions are added in the solvent to neutralize
the system. Then as everybody suggest, the ligand partial
I would suggest that you take Chris' advice and post all of this as a feature
request on redmine.gromacs.org so that it can be put on a to-do list. Enhancing
the performance of the free energy code is probably going to be a low-priority,
long-term goal (in the absence of any proven bug), but
Ok. I agree with you, FEP performance is an important issue to resolve but I
know that there are also other priorities. However, I would thank you for your
interest and and your suggestions.
Luca
I would suggest that you take Chris' advice and post all of this as a
feature request on
I followed your suggestions and i tried to perform a MD run wit GROMACS and
NAMD for dialanine peptide in a water box. The cell side cubic box was 40 A.
GROMACS:
With the free energy module there is a drop in gromacs performance of about
10/20 fold.
Standard MD: Time: 6.693
Hi,
This doesn't sound like normal behavior. In fact, this is not what I
typically observe. While there may be a small performance difference,
it is probably at the level of a few percent. Certainly not a factor
of more than 10.
You may want to provide an mdp file and topology, etc. so someone
David Mobley wrote:
Hi,
This doesn't sound like normal behavior. In fact, this is not what I
typically observe. While there may be a small performance difference,
it is probably at the level of a few percent. Certainly not a factor
of more than 10.
I see about a 50% reduction in speed when
I posted my test files in:
https://www.dropbox.com/link/17.-sUcJyMeEL?k=0f3b6fa098389405e7e15c886dcc83c1
This is a run for a dialanine peptide in a water box.
The cell side cubic box was 40 A.
The directory is organized as :
TEST\
topol.top
Run-00/confout.gro; Equilibrated
I don't know if it is possible or not. I think that you can enhance
your chances of developer attention if you develop a small and simple
test system that reproduces the slowdown and very explicitly state
your case for why you can't use some other method. I would suggest
posting that to
Dear all,
when I run a single free energy simulation
i noticed that there is a loss of performace with respect to
the normal MD
free_energy= yes
init_lambda= 0.9
delta_lambda = 0.0
couple-moltype = Protein_Chain_P
couple-lambda0 = vdw-q
couple-lambda0 = none
couple-intramol= yes
If we accept your text at face value, then the simulation slowed down
by a factor of 1500%, certainly not the 16% of the load balancing.
Please let us know what version of gromacs and cut and paste your
cammands that you used to run gromacs (so we can verify that you ran
on the same number
Hi Chris,
thank for the suggestions,
in the previous mail there is a mistake because
couple-moltype = SOL (for solvent) and not Protein_chaim_P.
Now the problem of the load balance seems reasonable, because
the water box is large ~9.0 nm.
However the problem exist and the performance loss is
Luca Bellucci wrote:
Hi Chris,
thank for the suggestions,
in the previous mail there is a mistake because
couple-moltype = SOL (for solvent) and not Protein_chaim_P.
Now the problem of the load balance seems reasonable, because
the water box is large ~9.0 nm.
Now your outcome makes a lot
Load balancing problems I can understand, but why would it take longer
in absolute time? I would have thought that some nodes would simple be
sitting idle, but this should not cause an increase in the overall
simulation time (15x at that!).
There must be some extra communication?
I agree
Dear Chris and Justin
Thank you for your precious suggestions
This is a test that i perform in a single machine with 8 cores
and gromacs 4.5.4.
I am trying to enhance the sampling of a protein using the decoupling scheme
of the free energy module of gromacs. However when i decouple only the
Luca Bellucci wrote:
Dear Chris and Justin
Thank you for your precious suggestions
This is a test that i perform in a single machine with 8 cores
and gromacs 4.5.4.
I am trying to enhance the sampling of a protein using the decoupling scheme
of the free energy module of gromacs.
Dear Chris and Justin
/ Thank you for your precious suggestions
// This is a test that i perform in a single machine with 8 cores
// and gromacs 4.5.4.
//
// I am trying to enhance the sampling of a protein using the decoupling
scheme
// of the free energy module of gromacs. However
Chris Neale wrote:
Dear Chris and Justin
/ Thank you for your precious suggestions
// This is a test that i perform in a single machine with 8 cores
// and gromacs 4.5.4.
//
// I am trying to enhance the sampling of a protein using the decoupling scheme
// of the free energy module
Yes i am testing the possibility to perform an Hamiltonian-REMD
Energy barriers can be overcome increasing the temperature system or scaling
potential energy with a lambda value, these methods are equivalent.
Both have advantages and disavantages, at this stage it is not the right place
to
Hi all,
I have been testing the ability of taking a sphere of a protein around a ligand, and positionally restrain the specified alpha carbons. I was hoping to keep non connected protein chains from drifting apart. I have been able to run these md/fep jobs, but I get huge
On 13/02/2011 11:49 AM, TJ Mustard wrote:
Hi all,
I have been testing the ability of taking a sphere of a protein around
a ligand, and positionally restrain the specified alpha carbons. I was
hoping to keep non connected protein chains from drifting apart. I
have been able to run these
On 13/02/2011 3:57 PM, TJ Mustard wrote:
On February 12, 2011 at 5:35 PM Mark Abraham mark.abra...@anu.edu.au
wrote:
On 13/02/2011 11:49 AM, TJ Mustard wrote:
Hi all,
I have been testing the ability of taking a sphere of a protein
around a ligand, and positionally restrain the
On February 12, 2011 at 5:35 PM Mark Abraham mark.abra...@anu.edu.au wrote:
On 13/02/2011 11:49 AM, TJ Mustard wrote:
Hi all,
I have been testing the ability of taking a sphere of a protein around
On February 12, 2011 at 9:31 PM Mark Abraham mark.abra...@anu.edu.au wrote:
On 13/02/2011 3:57 PM, TJ Mustard wrote:
On February 12, 2011 at 5:35 PM Mark Abraham
On 13/02/2011 5:03 PM, TJ Mustard wrote:
On February 12, 2011 at 9:31 PM Mark Abraham mark.abra...@anu.edu.au
wrote:
On 13/02/2011 3:57 PM, TJ Mustard wrote:
On February 12, 2011 at 5:35 PM Mark Abraham
mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote:
On 13/02/2011
On February 12, 2011 at 10:14 PM Mark Abraham mark.abra...@anu.edu.au wrote:
On 13/02/2011 5:03 PM, TJ Mustard wrote:
On February 12, 2011 at 9:31 PM Mark Abraham
On 13/02/2011 6:07 PM, TJ Mustard wrote:
On February 12, 2011 at 10:14 PM Mark Abraham
mark.abra...@anu.edu.au wrote:
On 13/02/2011 5:03 PM, TJ Mustard wrote:
On February 12, 2011 at 9:31 PM Mark Abraham
mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote:
On 13/02/2011
Hello!
I am new to this list, probably someone has have the same problem I
am facing now with the use of Gromacs to calculate FEP (Free energy
pertubaion).
I've followed the gromacs tutorial for Free energy Calculation
available at
On October 20, 2010 at 9:22 PM Marcelo Brando brandao.marc...@gmail.com wrote:
Hello!
I am new to this list, probably someone has have the same problem I
am facing now with the use of Gromacs to calculate FEP (Free energy
pertubaion).
TJ Mustard wrote:
On October 20, 2010 at 9:22 PM Marcelo Brandão
brandao.marc...@gmail.com wrote:
Hello!
I am new to this list, probably someone has have the same problem I
am facing now with the use of Gromacs to calculate FEP (Free energy
pertubaion).
I've followed the
I would have this in my production mdp files, or something like it:
; Free energy control stuff
free-energy = yes ; = no
init-lambda = XXX ; = 0
delta-lambda = 0 ; = 0
foreign_lambda = ; =
sc-alpha = 0.5 ; = 0
sc-power = 1.0 ; = 0
sc-sigma =
:
- Original Message -
From: TJ Mustard musta...@onid.orst.edu
Date: Tuesday, September 14, 2010 10:54
Subject: [gmx-users] FEP top file setup...
To: gmx-users@gromacs.org gmx-users@gromacs.org
I am tryng to run free energy perturbation (FEP) calculations on several ligands in several proteins. My problem is getting the correct B state atoms and charges for AMBER forcefields. If anyone can point me in the correct direction, that would be great.
I have read the
- Original Message -
From: TJ Mustard musta...@onid.orst.edu
Date: Tuesday, September 14, 2010 10:54
Subject: [gmx-users] FEP top file setup...
To: gmx-users@gromacs.org gmx-users@gromacs.org
---
|
I am
...
Thank you for any hint you could give me!
matteo
Date: Wed, 16 Jun 2010 15:17:30 +0200
From: Matteo De Chiara matn...@gmail.com
Subject: Re: [gmx-users] FEP for amino acid mutations.
To: gmx-users@gromacs.org
Message-ID:
aanlktikbum3htgngls6mo-cjl-buehpgeifdrhvk3...@mail.gmail.com
...@pharm.monash.edu.au
Subject: RE: [gmx-users] FEP for amino acid mutations.
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID:
89907ea1dcfb7548a431c13a270f9dd50ad84...@prk-exch-01.vcp.local
Content-Type: text/plain; charset=us-ascii
I would make a new residue in the .rtp file
Dear GROMACS users,
I would like to perform a FEP calculation mutating a residue outside
the active site of a protein.
I was wondering if I have to create a .itp file for the mutation or it
is possible to modify the .rtp file ( adding the state B parameter to
the amino acid I would like to
-users] FEP for amino acid mutations.
Dear GROMACS users,
I would like to perform a FEP calculation mutating a residue outside
the active site of a protein.
I was wondering if I have to create a .itp file for the mutation or it
is possible to modify the .rtp file ( adding the state B parameter
Hi
I am simulating a system consisting of a protein embedded in membrane,
solvated with water using the Martini forcefield. I have set up a free
energy perturbation simulation where a subset of the protein particles are
being converted from their original particle type (state A, lambda =0) to a
Those derivatives should be zero: the kinetic energy is determined by your
thermostat and shouldn't change as a function of lambda - as it should for any
normal free energy calculation in constant-temperature ensembles.
Also, the constraint energy doesn't change as lambda changes (only the van
Hi,
how can I use different coulomb 1-4 interactions in the A and B state.
The Manual just says
[ pairs ] : LJ and Coulomb 1-4 interactions
but, I far as I could see, did not give an example how the coulomb 1-4
interaction can be explicitly given.
Thanks a lot for any help,
Jochen
--
Hi,
There are automatically different, since they are based on the A and B state
charges
and the A and B state atom types.
Berk
Date: Thu, 19 Nov 2009 16:15:52 +0100
From: joc...@xray.bmc.uu.se
To: gmx-users@gromacs.org
Subject: [gmx-users] FEP with bond formation, pair problem
Hi
). Then the interactions
that are non-bonded in the A state are excluded in the B state and
replaced by pair interactions.
Is this supported in some way?
Berk
Date: Thu, 19 Nov 2009 16:15:52 +0100
From: joc...@xray.bmc.uu.se
To: gmx-users@gromacs.org
Subject: [gmx-users] FEP
To: gmx-users@gromacs.org
Subject: [gmx-users] FEP with bond formation, pair problem
Hi,
how can I use different coulomb 1-4 interactions in the A and B
state.
The Manual just says
[ pairs ] : LJ and Coulomb 1-4 interactions
but, I far as I could see, did not give an example how
I have performed FEP calculations by averaging backward and forward
perturbations in intervals of 0.05 regarding lambda. The averages between
each of these sets of perturbations were summed to obtain the final free
energy with respect to that particular mutation. I have tryed to obtain the
error
I agree with Carsten. See perhaps the discussion at www.alchemistry.org as
well.
On Fri, Aug 7, 2009 at 2:35 AM, Carsten Kutzner ckut...@gwdg.de wrote:
On Aug 6, 2009, at 10:57 PM, Ragnarok sdf wrote:
I am performing FEP do obtain the dimerization of a protein in
membrane. The lambda
I am performing FEP do obtain the dimerization of a protein in
membrane. The lambda intervals i am using are 0.05 for each window.
After that I rerun each lambda .trr perturbing the system (plus)0.05
and (minus)0.05 lambda value. Then with g-energy I obtain the deltaG
for each delta lambda.
Well,
Hello GMX-people
I am trying to locate the source code files regarding free energy
perturbation (FEP) calculations. Does anyone have an idea?
regards,
--
Murat Cetinkaya, PhD
Max-Planck-Institute for Metals Research
Protein Mechanics and Evolution Group
Bioquant BQ0031, Universitaet
a
grep -rl -e FEP -e dvdlambda *
in the gromacs source directory will show you these files.
Carsten
On Apr 24, 2009, at 4:33 PM, murat cetinkaya wrote:
Hello GMX-people
I am trying to locate the source code files regarding free energy
perturbation (FEP) calculations. Does anyone have an
Hi
This warning is really strange.
You could try to execute grompp with -pp to get the preprocessed
topology and have a look, if the the B-parameters are included
correctly. As far as I know, it should; I do it the same way.
Anyway, you could also explicitly take the parameters for that
Thanks Maik for your parameters for amber99 soft core !
Berk, you were right. The missing term is indeed the one associated to the use
of constraints=all-bonds. And yes, there was a mistake in my .top file...
May I ask an other question ?
I still have a warning message with grompp :
WARNING
Hi,
I would like to know if there is a way to see the values of each components
(angles, dihedrals, Coulomb...) of dgdl when performing FEP, to check whether I
correctly defined the topology of state B.
Many thanks,
Michael Bon
winmail.dat___
Yep, all atoms begin to freezeeven the ones not being perturbed
(i.e. the water molecules). It's pretty strange. It only happens for
lambda=1.0. Below is my .mdp file.
; Run Control
integrator = md ; calculation type
dt = 0.0015
The distortion was occuring because my position restraint potential
was too weak. Increasing the force constant keeps the base in the
right conformation.
I believe my topology is correct, but it seems that turning off the
VdW parameters causes the base to distort. I will look into this more.
Thank you David and Maik for your detailed replies. Yes, I am trying
to obtain an absolute free energy of binding. My thermodynamic cycle
is:
NT+DNA(adsorbed) - NT+ DNA(desorbed) (obviously this is not the one
that I'm obtaining with the alchemic method)
Thus, the one I'm using in the
Robert
I think, I cant help you too much, cause your problem involves too many
sources of errors.
Your topology (if continued that way) seems to be ok.
Your TI-params seem to be ok, too.
First, make clear: Do you use Position RESTRAINTS or (distance)
CONSTRAINTS. There is a fundamental
Robert,
I'm computing the free energy of binding of a DNA base on a carbon
nanotube. I think it's a pretty simple calculation and I'm proceeding
in a very standard way. This is what I'm doing:
An absolute free energy? This isn't necessarily straightforward --
there are a lot of wrinkles. Some
Hello everyone,
I'm computing the free energy of binding of a DNA base on a carbon
nanotube. I think it's a pretty simple calculation and I'm proceeding
in a very standard way. This is what I'm doing:
I have the optimal orientation of the base on the nanotube. I'm
constraining the positions of
[EMAIL PROTECTED] wrote:
Hi,
I would like to perform free energy perturbation using gromacs.
I found some tutorial about this type of calculation, but a question is
not clear.
My calculation is very similar to the calculation described in the
tutorial, because I want to change only the non
Hi,
I would like to perform free energy perturbation using gromacs.
I found some tutorial about this type of calculation, but a question is
not clear.
My calculation is very similar to the calculation described in the
tutorial, because I want to change only the non bonded terms.
I didn't
Thank you David, I really appreciated your help. I will read your paper and
try to go on.
Thank you very much!
2007/7/27, David Mobley [EMAIL PROTECTED]:
Hi,
I am trying to run some simulations in attempts to calculate binding
free
energy between ligands and a protein using the FEP
Hi,
I am trying to run some simulations in attempts to calculate binding free
energy between ligands and a protein using the FEP method, but until now I
did not have any success. I have been looking for bibliography over this
subject, but, as you may know, there aren't many works about FEP.
Thanks again for the reply. A virtual point charge
is what I want.
Best wishes
George
-Original Message-
From: [EMAIL PROTECTED] on behalf of Maik Goette
Sent: Wed 5/23/2007 12:51 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] FEP with real or dummy charges
I don't really know, if this may solve your problem, but what I want to
suggest is, not using PME for the simulation. I don't know, how other
longerange-methods behave while changing the total charge of the system,
PME won't work (as far, as I know).
Concerning your way, how to perturb the
Hi
I want to calculate the change in free energy (electrostatic contribution only)
when introducing a charge in a certain site of a protein using a single step
FEP.
Should this be done with charging an inserted virtual site (a dummy atom) or a
protein atom (e.g. Ca)?
I noticed that in the
Hi all
Because the fact of handling vdw and electrostatics with the same values
was discussed before, I won't go into much detail about what Berk and
David M. wrote.
I changed the code to apply different alpha values for vdw and
electrostatics. Now I am able to e.g. calculate vdw with an
Hi David
Thank you for the detailed answer.
It sounds reasonable. :)
For sure it's the best way to make the calculations separatly and sum up
the energies at the end. You mentioned, that, in the case of splitting,
the density of snapshot samplings at lambda=0,1 can be lower.
So I guess, one
From: Maik Goette [EMAIL PROTECTED]
Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org
To: Discussion list for GROMACS users gmx-users@gromacs.org
Subject: Re: [gmx-users] FEP softcore problematics
Date: Wed, 21 Jun 2006 14:55:34 +0200
Hi David
Thank you for the detailed
: [gmx-users] FEP softcore problematics
Date: Wed, 21 Jun 2006 14:55:34 +0200
Hi David
Thank you for the detailed answer.
It sounds reasonable. :)
For sure it's the best way to make the calculations separatly and sum
up the energies at the end. You mentioned, that, in the case of
splitting
From: Alexandra Patriksson [EMAIL PROTECTED]
Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org
To: gmx-users@gromacs.org
Subject: [gmx-users] fep calculation of L-Asn - D-Asn transition
Date: Wed, 24 May 2006 11:11:38 +0200
Dear all,
I'm trying to do a fep calculation
Hi allIm doing FEP calculation on Zn
ions.Is three a way to put position restraints on perturbated /
dummy atoms.When I define in my system.top:
#include "zn.itp"[
position_restraints ]; i funct
fcx
fcy fcz
1 1
1000
1000 1000
#include "cl.itp"[ position_restraints
]; i funct
fcx
Right. Thank you for help.
Now it works fine.
:)
- Original Message -
From: Berk Hess [EMAIL PROTECTED]
To: gmx-users@gromacs.org
Sent: Thursday, April 06, 2006 6:02 PM
Subject: RE: [gmx-users] FEP and position restraints
From: P [EMAIL PROTECTED]
Reply-To: Discussion list
Hi all.Im trying FEP In gromacs3.3. My
system (3nm; 3nm; 3nm) consists of one Na, Cl, DUM ion and solvent
molecules. During my free energy calculations I want to perturb:1)
Cl- into a DUM atom2) DUM into
Cl-
Im using ffgmx. Ive added new atom DUM into
ffgmx.atp:.. SD 32.06000 ;
DMSO
Mark,
I am rather nervous about doing FEP/TI for disappearing charged molecules, as it is not at all clear to me that it is possible do this
correctly with current methods. Perhaps someone else may be able to comment more, but at least with long range electrostatics (PME), systems are required
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