Thanks for your reply, Stephan.
Did the molecule you worked with have any atoms that are isolated
(non-bonded) to the others?
Was the equilibration run in your 1st case just a way to recruit those
isolated atoms to the others in the same molecule? I suspect I might need
to add artificial bond to c
On 5/9/12 10:37 PM, DeChang Li wrote:
Dear all,
I want to calculate the ion solvation free energy (e.g. an ion
Na+ solvated in a water box) using Bennett Acceptance Ratio (BAR)
method, following the tutorial by Justin A. Lemkul. However, if I turn
off the Coulombic interaction, the tota
Chunxia Gao wrote:
Dear gmx users:
I am using the free energy to calculate the ligand binding affinity to protein,
during the decouple process, I need to put some restraint between the protein
and the ligand, e.g. distance restraint.
But distance restraint is only for intramolecular, so I
Fabian Casteblanco wrote:
Hello Justin,
I'm calculating the free energy of a drug in an alcohol solvent. I
have a question referring to your free energy tutorial. You mentioned
that decoupling of electrostatic interactions is linear and decoupling
of vdW can vary. Is this true for your case
Fabian Casteblanco wrote:
Hello all,
I am setting up a free energy calculation (drug from full coulomb+vdW
in solution --> drug with only vdW in solution --> dummy drug in
solution).
After reading most of the papers, I understand that you need
significant overlap from the energies for each in
Anirban Ghosh wrote:
Hello Justin,
Thanks a lot for the reply.
Yes, I am using GROAMCS 4.5 and my system consists of two chains of two
proteins, a substrate and an inhibitor solvated in water. So can you
please tell me what should be the values for:
couple-moltype
The name of
Hello Justin,
Thanks a lot for the reply.
Yes, I am using GROAMCS 4.5 and my system consists of two chains of two
proteins, a substrate and an inhibitor solvated in water. So can you please
tell me what should be the values for:
couple-moltypecouple-lambda0couple-intramolThanks a lot again.
Rega
Anirban Ghosh wrote:
Hi ALL,
I am trying to run free energy calculation and for that in the md.mdp
file I am keeping the following option:
; Free energy control stuff
free_energy = yes
init_lambda = 0.0
delta_lambda= 0
sc_alpha=0.5
sc-power=1.0
sc-sigma=
Павел Кудрявцев wrote:
Hi,
I wanna perform free energy calculation by changing parameters of
amino acid residue. Since my case is rathe complicated first I tried
to perform a very simplified task - to change only charges of atoms.
So I peeked out one residue, keeped all its atom types and mass
>> Hello, dear users!
>>
>> I want to study different components in total free energy.
>> Could you tell me in what gromacs program and in what place exactly force
and energy are calculated?
>I think your question is too general. I don't know whether you've already
done a calculation, are planning
- Original Message -
From: Петр Попов
Date: Thursday, September 30, 2010 22:39
Subject: [gmx-users] Free Energy Calculation
To: gmx-users@gromacs.org
> Hello, dear users!
>
> I want to study different components in total free energy.
> Could you tell me in what gromacs program and in w
Hi Anirban,
You *could* use the configurations in your trajectory to (re)calculate average
energies; by de-coupling your ligand this would get you the average free energy
change per coupling strength change at the point where the ligand is fully
bound.
If you're interested in free energy of bi
So, obviously, no one knows how to do that by g_lie. Most people here
compute free energies by TI.
Do some background reading and find out yourself how it works. Posting
mails twice or more won't help you
regards
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoret
gy calculation
>
> Hello everyone,
>
> Here i want to caculate the binding free energy between an ligand and its
> receptor. Should I set free_energy as "yes" in Free Energy Perturbation Part
>
> or use g_lie by doing recepto-ligand-solvate md and ligand-solvate md
&
Quoting shuai lu <[EMAIL PROTECTED]>:
> Hello everyone,
>
> Here i want to caculate the binding free energy between an ligand and its
> receptor. Should I set free_energy as "yes" in Free Energy Perturbation Part
Yes, among other things. Read the manual regarding all the free energy options.
Si
I bet, this topic has been discussed on the list multiple times before.
Numerical Integration is the keyword here and be aware of the problems
in calculating the total error from the single errors (look into Shirts
papers).
I suggest to inform yourself intensively about free energy calculation
Hi,
> I need to calculate the free energy of complex formation between protein A
> and ligand B. I am about to simulate in solution the molecular dynamics of A,
> B and AB complex separately and calculate the free energy of each system
> using g_lie. Then, I suppose, deltaG = G(AB) - (G(A) + G(
Why not do a steered MD or umbrella sampling, where you start with the
ligand in the binding pocket (in its correct conformation) and gradually
pull it out. If done correctly, you should get a nice PMF.
> Hello!
> I need to calculate the free energy of complex formation between protein A
> and li
Hello,
What I want to do is calculate the free energy difference of pulling the
ligand away from the receptor. I want to do it using theromdynamic
intergration using the Lamda 0/1 stuff. I am just not clear of the
procedure of how to do it.
I want to constraint several distances between the ligan
Sorry, I really didn't get, what your goal is and what, in fact, you
really want to do.
For free energy calculations, you can
- either do Thermodynamic integration (the lambda 0/1 stuff)
- or pulling (force probe) and afterwards use Jarzynskis theorem
- or umbrella sampling together with WHAM (i
Hi,
You are probably starting your runs from a non equilibrated structure.
I don't think this is necessarily true: For example, you could be
seeing the crash you describe on the first step of equilibration...
However, you might want to make usre you have thoroughly *minimized*
at each lambda v
You are probably starting your runs from a non equilibrated structure.
Assume, the system changes via a slow growth run.
The atoms may rearrange due to changes in their potentials.
Therefore it may be problematic, if you start from the same structure
for different lambdas. Try simulating a one wa
--- David Mobley <[EMAIL PROTECTED]> wrote:
> What I've shown in my work is that at some particular lambda values,
> there maybe worse sampling problems than at any other lambda value.
> This means that you may need to run longer at that particular lambda
> value in order to get adequate statistic
Ignacio,
OK, I do basically the same, but instead of starting the second
equilibration from the same structure for each lambda, I start from the
final structure of the previous lambda (still, I equilibrate before
production for each lambda). I don't see why this strategy should be
worse the one
Ignacio Fernández Galván a écrit :
--- David Mobley <[EMAIL PROTECTED]> wrote:
[...]
In terms of implementation, what I do is I prepare a particular
equiliibrated structure of my system in water. Then I set up run
input
files for all of my different lambda values, and I then minimize and
equil
David Mobley a écrit :
Stéphane,
I'm willing to do some FEP using the slow groth approach available in
gromacs (as of 3.3.1). While retrieving articles and the mailing list, i
found out there where arguments against sequential runs (particularly
for avoiding the hysteresis problem), and other
--- David Mobley <[EMAIL PROTECTED]> wrote:
> [...]
>
> In terms of implementation, what I do is I prepare a particular
> equiliibrated structure of my system in water. Then I set up run
> input
> files for all of my different lambda values, and I then minimize and
> equilibrate my system AGAIN at
Stéphane,
I'm willing to do some FEP using the slow groth approach available in
gromacs (as of 3.3.1). While retrieving articles and the mailing list, i
found out there where arguments against sequential runs (particularly
for avoiding the hysteresis problem), and other against parallel runs.
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