Dear Kieu Thu
Thanks for your comment about free energy. Unfortunately, I could not send a
email to Paissoni Cristina in the Gromacs Forum.
Could you give me email address of Paissoni Cristina? Finding a tool for
calculation MM/PBSA with Gromacs is very vital for me.
Best Regards
Kiana
--
View
On 6/23/13 1:13 AM, Dwey wrote:
Hi Justin,
Thank you for sharing your experience with me.
As suggested, Gromacs ver 4.5.5 is compiled within the same Linux box
and I am able to reproduce a similar result ( DG= -9.30 kJmol-1).
Gromacs ver 4.5.5 and 4.6.2 both are compiled from source
Hi Justin,
Thank you for sharing your experience with me.
As suggested, Gromacs ver 4.5.5 is compiled within the same Linux box
and I am able to reproduce a similar result ( DG= -9.30 kJmol-1).
Gromacs ver 4.5.5 and 4.6.2 both are compiled from source codes, while
Gromacs ver 4.5.7 as
Thanks Justin and Professor Shirts. The gmxdump on the resulting tpr did
indeed solve a lot of my problems. Thanks again.
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View this message in context:
http://gromacs.5086.x6.nabble.com/Free-Energy-Calculations-in-Gromacs-tp5007495p5009115.html
Sent from the GROMACS Users Forum mailing
Hi,
I have been trying to perform the simulations using the amber forcefield, in
which the [ pairtypes ] directive is not defined explicitly in the
ffnonbonded.itp file, but rather the 1-4 interactions are generated as per
the defaults section in the forcefield.itp file. I was wondering what
On 6/10/13 2:50 PM, JW Gibbs wrote:
Hi,
I have been trying to perform the simulations using the amber forcefield, in
which the [ pairtypes ] directive is not defined explicitly in the
ffnonbonded.itp file, but rather the 1-4 interactions are generated as per
the defaults section in the
An important final point is that you can always see EXACTLY what
grompp is putting into the B state by running gmxdump on the resulting
tpr. It's a LOT of information, but all in text all the interactions
are listed explicitly there.
On Mon, Jun 10, 2013 at 6:20 PM, Justin Lemkul jalem...@vt.edu
The BAR method calculates a ratio of weighted average of the Hamiltonian
difference of state B given state A and vice versa.
So, for different peptides, can this method apply to compare the stability
of peptides?
Thank you very much!
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Dear Justin,
Thanks for your response and the perfect tutorial. I found the details
I needed in it.
Best regards,
Sarah
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* Please search the archive at
Hello Justin,
I am running 2,000,000 time steps for the actual MD run (4,000 ps).
Depending on how many solvent molecules I start with, I get slightly
different results. Do you think its ok to run several different tests
and take the average? Or perhaps take the end results of a shorter MD
run
Fabian Casteblanco wrote:
Hello Justin,
I am running 2,000,000 time steps for the actual MD run (4,000 ps).
Depending on how many solvent molecules I start with, I get slightly
different results. Do you think its ok to run several different tests
and take the average? Or perhaps take the
Hello Justin,
I'm looking at the dG vs Lambda plot that is an output from G_bar but
on the Shirts et al paper that you included, the part where it talks
about linearity, it is referring to dH/dLambda for electrostatic
decoupling. So if I take the line formed by dGtotal vs Lambda from
g_bar
Fabian Casteblanco wrote:
Hello Justin,
I'm looking at the dG vs Lambda plot that is an output from G_bar but
on the Shirts et al paper that you included, the part where it talks
about linearity, it is referring to dH/dLambda for electrostatic
decoupling. So if I take the line formed by
Hello Justin,
You mean that only for vdW decoupling, you would need to use soft-core
potentials? I had soft -core potentials on for decoupling the
electrostatic interactions (see below). What would I use in its
place? Thanks again for your help!
;Production MD
Fabian Casteblanco wrote:
Hello Justin,
You mean that only for vdW decoupling, you would need to use soft-core
potentials? I had soft -core potentials on for decoupling the
electrostatic interactions (see below). What would I use in its
place? Thanks again for your help!
You only need
Thanks Justin!
On Wed, Aug 31, 2011 at 11:24 AM, Fabian Casteblanco
fabian.castebla...@gmail.com 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
Thanks Justin.
Best regards,
Fabian
On Mon, Aug 8, 2011 at 5:49 PM, Fabian Casteblanco
fabian.castebla...@gmail.com 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
Message: 1
Date: Tue, 05 Jul 2011 19:14:04 -0400
From: Justin A. Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] free energy calculations
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID: 4e139abc.1030...@vt.edu
Content-Type: text/plain; charset=ISO-8859-1;
Ragothaman Yennamalli wrote:
Message: 1
Date: Tue, 05 Jul 2011 19:14:04 -0400
From: Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu
Subject: Re: [gmx-users] free energy calculations
To: Discussion list for GROMACS users gmx-users@gromacs.org
Moeed,
Sorry for the late response, and yes I did need to include more information in my answer.
1) If your polymers are physically close together in reality you might want to have multiple polymers in a single FEP job.
I run single ligands
hello
Now it is almost clear what happened. When couple-intramol is no (default),
all pairwise vdm and charge interaction becomes bonded interaction.
All intra-molecular non-bonded interactions for moleculetype couple-moltype
are replaced by exclusions and explicit pair interactions. In this
hi,
I did more test and found that it depended on size of the protein. Grompp
will die when number of atoms of the protein is larger than about 200. Is it
possible the source code limit the size of the protein that can be
decoupled?
thanks.
dawei
On Mon, Feb 7, 2011 at 10:34 AM, Da-Wei Li
Well. It actually isn't dead but becomes very slow for large proteins.
dawei
On Mon, Feb 7, 2011 at 11:44 AM, Da-Wei Li lida...@gmail.com wrote:
hi,
I did more test and found that it depended on size of the protein. Grompp
will die when number of atoms of the protein is larger than about
Dawei,
I have no problems with proteins in the thousands of atoms. Can you post your command line and mdp files?
Thank you,
TJ Mustard
On February 7, 2011 at 9:31 AM Da-Wei Li lida...@gmail.com wrote:
Well. It
Da-Wei Li wrote:
hello
Here they are the command line and mdp file. I use Gromacs 4.5.3. This
is a test case only and the protein is 1UBQ. Grompp wills top for about
10 minutes then go through.
The efficiency of this kind of process will depend on the amount of available
memory on the
Da-Wei,
Do you need FEP information on the PR step? Are you going to do a MD(sd) with FEP on after the PR?
And are you doing hydration of a protein?
Thank you,
TJ Mustard
On February 7, 2011 at 10:23 AM Justin A. Lemkul
hello
My goal is to study the solvation free energy of a fixed protein and compare
it with implicit model. The pr1. mdp is just a test case. Grompp always need
more than 10 minutes to finish for my 76 residues protein when free_energy =
yes, no matter there is PR or not, whether I switch off only
hi, all
I get another strange error. Once I turn on free energy calculation. mdrun
will complain this:
Initial maximum inter charge-group distances:
two-body bonded interactions: 4.509 nm, LJC Pairs NB, atoms 1013 1231
multi-body bonded interactions: 0.428 nm, Proper Dih., atoms 5 13
Da-Wei,
How do you generate your box, solvent, ions?
I use this sequence of commands:
pdb2gmx -f protein.pdb -o protein.gro -p protein.top
editconf -bt cubic -f protein.gro -o protein.gro -c -d 1.5
genbox -cp protein.gro -cs spc216.gro -o
Da-Wei Li wrote:
hi, all
I get another strange error. Once I turn on free energy calculation.
mdrun will complain this:
Initial maximum inter charge-group distances:
two-body bonded interactions: 4.509 nm, LJC Pairs NB, atoms 1013 1231
multi-body bonded interactions: 0.428 nm, Proper
hello
1. I used almost identical comands with you.
2. If I set couple-intramol = yes. My grompp will run very fast.
From the manu, couple-intramol = no means all intramol (protein-protein
interaction in my case) interaction are turned to predefind list while
couple-intramol
Da-Wei Li wrote:
hello
1. I used almost identical comands with you.
2. If I set couple-intramol = yes. My grompp will run very fast.
From the manu, couple-intramol = no means all intramol
(protein-protein interaction in my case) interaction are turned to
predefind list
Hi Justin,
thanks for this link:
http://lists.gromacs.org/pipermail/gmx-users/2003-June/006054.html
It clearly says, why sampling by MD is not proper.
Best,
Eva
Hello all,
I am trying calculate desolvation free energy of Na+ in water using
option
couple-moltype, not by creating
to having
this method in GROMACS?
best wishes,
Floris
From: Berk Hess g...@hotmail.com
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Friday, 7 August, 2009 16:16:19
Subject: RE: [gmx-users] Re: Free Energy Calculation
All the discussion
are much less severe
than the issues with Berendsen temperature coupling. Berendsen tcoupl can have
significant effects on your ensemble. But in Gromacs 4.0 this can easily be
avoided
by using the v-rescale thermostat.
Berk
Subject: RE: [gmx-users] Re: Free Energy Calculation
Date: Thu, 6 Aug 2009
...@gromacs.org on behalf of David Mobley
Sent: Thu 8/6/2009 2:38 PM
To: Mauricio Carrillo Tripp
Cc: Discussion list for GROMACS users
Subject: [gmx-users] Re: Free Energy Calculation
Hi,
Sorry for the delay answering. These questions are better put on the
GROMACS users list.
1) Yes
. Berendsen tcoupl can
have
significant effects on your ensemble. But in Gromacs 4.0 this can easily be
avoided
by using the v-rescale thermostat.
Berk
--
Subject: RE: [gmx-users] Re: Free Energy Calculation
Date: Thu, 6 Aug 2009 16:01:04 -0400
From: pn
Subject: RE: [gmx-users] Re: Free Energy Calculation
Date: Thu, 6 Aug 2009 16:01:04 -0400
From: pn...@utnet.utoledo.edu
To: gmx-users@gromacs.org
A question to the answer below:
If the Berendsen barostat does not sample correctly the distribution of
pressures
then what
ago.
Berk
Date: Fri, 7 Aug 2009 07:32:33 -0700
From: floris_buel...@yahoo.com
Subject: Re: [gmx-users] Re: Free Energy Calculation
To: gmx-users@gromacs.org
Hi David and Berk,
I guess the best proper solution would be to use a Parrinello-Rahman barostat.
But in Gromacs this is currently
Hi,
Sorry for the delay answering. These questions are better put on the
GROMACS users list.
1) Yes -- the Berendsen barostat does not sample the correct
distribution of pressures.
2) Regenerating velocities is fine for a couple of reasons: (a) we are
after thermodynamics, not dynamics,
-Original Message-
From: gmx-users-boun...@gromacs.org on behalf of David Mobley
Sent: Thu 8/6/2009 2:38 PM
To: Mauricio Carrillo Tripp
Cc: Discussion list for GROMACS users
Subject: [gmx-users] Re: Free Energy Calculation
Hi,
Sorry for the delay answering. These questions are better
You may also want to look at www.alchemistry.org, as it has some
general information about how these should be set up.
On Wed, Mar 18, 2009 at 8:02 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Again, *please keep all Gromacs-related correspondence on the mailing list*
The type of information
Eudes Fileti wrote:
Hello Justin,
I am facing a very similar problem to that you experienced and described
in (http://www.gromacs.org/pipermail/gmx-users/2008-February/032429.html).
I throw this question in the GMX forum and Berk has kindly helped me.
But reading the forum I realized that
Again, *please keep all Gromacs-related correspondence on the mailing list* The
type of information that you have posted is important to share with others who
may know how to help. I do not know the answer to your problem. I would
suggest contacting the list again with the following
Berk,
Any chance of getting a fix for 3.3.x versions also? I have several
papers which probably are affected by this problem and I will need to
repeat the calculations with a fixed version and produce errata. I
would prefer to do this with 3.3.x since (a) not all of the data is
with
-users] Re: free energy with TIP4P bug fixed
Berk,
Any chance of getting a fix for 3.3.x versions also? I have several papers
which probably are affected by this problem and I will need to repeat the
calculations with a fixed version and produce errata. I would prefer to do this
with 3.3.x since
From: g...@hotmail.com
To: gmx-users@gromacs.org
Subject: RE: [gmx-users] Re: free energy with TIP4P bug fixed
Date: Thu, 29 Jan 2009 13:48:20 +0100
Hi,
You can apply the cvs diff.
But even simpler, as I said, is just putting your solute and solvent in
separate charge** groups.
** I
Hello all
I have tried to reproduce the hydration free energy (TI) of the ethanol
from Hess and van der Vegt (JPCB, 110, 17616).
The value I have obtained is around 20kJ/mol while the reference value
is -20.1kJ/mol (if not the sign ...).
If someone can help me find the mistake I
Dear Eudes,
I don't have time to provide personalized help with this at present.
You'll be better off writing the gromacs forum. You may also want to
refer to the general information on performing free energy
calculations at http://www.alchemistry.org and previous posts on the
gromacs users list.
Hi,
I am traveling and don't have time to answer this now, nor am I
responsible for the tutorial you mention. I also only usually answer
questions like this on the gromacs users list, not in my personal
e-mail.
I suggest you direct your e-mail to the Gromacs users list (which I am
ccing on this)
Dear all,
Can anybody tell me how to calculate the free energy difference after
running simulation with lamda(0, 0.1,...1)?
I am following the tutorial on wiki, but i have no idea about the
details to do the data analysis.
any software can do it? and any reference for the instruction? I am new
David Mobley wrote:
Bharat, Matt, Tsjerk, and all,
I just put a bit of a tutorial on free energy calculations up at
http://www.dillgroup.ucsf.edu/~jchodera/group/wiki/index.php/Free_Energy:_Tutorial.
This will probably be a work in progress; it is not as step-by-step as
Tsjerk's (although
Bharat, Matt, Tsjerk, and all,
I just put a bit of a tutorial on free energy calculations up at
http://www.dillgroup.ucsf.edu/~jchodera/group/wiki/index.php/Free_Energy:_Tutorial.
This will probably be a work in progress; it is not as step-by-step as
Tsjerk's (although possibly I could make it
Hi Bharat and Matt,
The tutorial was set up by a colleague of mine, who has left our group
a while ago. Given your remarks, I think it's better to replace the
current version with a new one. I hope I can find some time for the
revision and would welcome any suggestions for changes, additions
Hi Bharat,
This is the same tutorial that led me astray when I first began trying free
energy
calculations in Gromacs. I am not sure how close to the experimental value the
author
intended to get with this hydration free energy tutorial. If you are using a
recent
version of Gromacs, be aware
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