Dear all,
I am looking how I can extract the interaction energy between specific
residue in a set of residues.
example:
I have DT and DA residues, I would like to plot only the energy of the DT.
I can extract the DT with the index file, But I am missing information on
how to plot the energy
On 7/31/13 4:20 PM, Collins Nganou wrote:
Dear all,
I am looking how I can extract the interaction energy between specific
residue in a set of residues.
Nonbonded energy terms are decomposed using energygrps in the .mdp file along
with suitable index groups.
example:
I have DT and
Dear All,
I want to calculate interaction energy per residue.
Below is the command i used:
g_enemat -f strand.edr -groups groups.dat -emat strand_emat.xpm
my groups.dat file contains these lines:
3
strand1_SER_34
strand1_THR_36
strand1_TYR_37
When i execute the above g_enemat command i get
On 7/24/13 7:47 AM, Poojari, Chetan wrote:
Dear All,
I want to calculate interaction energy per residue.
Below is the command i used:
g_enemat -f strand.edr -groups groups.dat -emat strand_emat.xpm
my groups.dat file contains these lines:
3
strand1_SER_34
strand1_THR_36
strand1_TYR_37
HI
I'm simulating gold-protein interaction by gromacs. after MD simulation I want
to calculate interaction energy of each aminoacids with
AU surface.
Enon-bond = E(vdw) + E(elec)
gold atoms charge in simulation were considered 0, then E non-bonded=E(vdw)
Is this true?
The interaction
On 4/18/13 2:00 AM, fatemeh ramezani wrote:
HI
I'm simulating gold-protein interaction by gromacs. after MD simulation I want
to calculate interaction energy of each aminoacids with
AU surface.
Enon-bond = E(vdw) + E(elec)
gold atoms charge in simulation were considered 0, then E
Dear Gromacs User,
I am simulating two constrained fullerenes to analyze the interaction energy
between these two in vacuum. To do that I specified energygrps in .mdp file as
CB1 and CB2 which corrospond to the residue name of first and second fullerene
respectively. The charge of the atoms of
On 12/2/12 10:38 PM, Mortuza Munna wrote:
Dear Gromacs User, I am simulating two constrained fullerenes to analyze the
interaction energy between these two in vacuum. To do that I specified
energygrps in .mdp file as CB1 and CB2 which corrospond to the residue name
of first and second
Hi justin,
As per your advice,
g_enemat -f ener.edr -groups groups.dat -nocoul -nolj
Opened ener.edr as single precision energy file
Will read groupnames from inputfile
Read 2 groups
group 0WARNING! could not find group (null):energy-energy (0,0)in energy
file
WARNING! could not find group
On 10/8/12 5:40 AM, rama david wrote:
Hi justin,
As per your advice,
g_enemat -f ener.edr -groups groups.dat -nocoul -nolj
Opened ener.edr as single precision energy file
Will read groupnames from inputfile
Read 2 groups
group 0WARNING! could not find group (null):energy-energy (0,0)in
Hi justin,
I correct command as follow and
g_enemat -f ener.edr -groups groups.dat -coul -lj
out-put is like
Opened ener.edr as single precision energy file
Will read groupnames from inputfile
Read 2 groups
group 0WARNING! could not find group (null):energy-energy (0,0)in energy
file
WARNING!
On 10/8/12 6:00 AM, rama david wrote:
Hi justin,
I correct command as follow and
g_enemat -f ener.edr -groups groups.dat -coul -lj
out-put is like
Opened ener.edr as single precision energy file
Will read groupnames from inputfile
Read 2 groups
group 0WARNING! could not find group
Hi justin,
g_enemat -f ener.edr -groups groups.dat -coul -nolj
Out-put is like
Opened ener.edr as single precision energy file
Will read groupnames from inputfile
Read 2 groups
group 0WARNING! could not find group (null):energy-energy (0,0)in energy
file
WARNING! could not find group
On 10/8/12 7:09 AM, rama david wrote:
Hi justin,
g_enemat -f ener.edr -groups groups.dat -coul -nolj
Out-put is like
Opened ener.edr as single precision energy file
Will read groupnames from inputfile
Read 2 groups
group 0WARNING! could not find group (null):energy-energy (0,0)in energy
Hi justin,
the out put of g_energy are like
-
1 G96Angle 2 Proper-Dih. 3 Improper-Dih.4
LJ-14
5 Coulomb-14 6 LJ-(SR) 7 LJ-(LR) 8
Disper.-corr.
9 Coulomb-(SR)10 Coul.-recip.
On 10/6/12 2:28 AM, rama david wrote:
Hi justin,
the out put of g_energy are like
-
1 G96Angle 2 Proper-Dih. 3 Improper-Dih.4
LJ-14
5 Coulomb-14 6 LJ-(SR) 7 LJ-(LR) 8
Hi justin,
I tried as per your suggestion.
command line
g_enemat -f ener.edr -groups groups.dat -temp 310 -nolj -free
the out put is like ,
Opened ener.edr as single precision energy file
Will read groupnames from inputfile
Read 2 groups
group 0WARNING! could not find group
On 10/6/12 6:26 AM, rama david wrote:
Hi justin,
I tried as per your suggestion.
command line
g_enemat -f ener.edr -groups groups.dat -temp 310 -nolj -free
the out put is like ,
Opened ener.edr as single precision energy file
Will read groupnames from inputfile
Read 2 groups
group
On 10/5/12 5:49 AM, rama david wrote:
Hi Friends,
I want to study the interaction energy between the selected residues of
protein and ligand.
( Non-bonded energy should include : vanderwall and electrostatics)
How to do it???
This is what the energygrps keyword in the .mdp file is for.
Hi justin,
I completed the simulation ,
Now I want to use the selected residues of protein and ligand.
How to do it
Would you explain me in detail??
With best wishes and regards,
Rama david.
On Fri, Oct 5, 2012 at 3:40 PM, Justin Lemkul jalem...@vt.edu wrote:
On 10/5/12 5:49 AM, rama david
On 10/5/12 6:15 AM, rama david wrote:
Hi justin,
I completed the simulation ,
Now I want to use the selected residues of protein and ligand.
How to do it
Would you explain me in detail??
Create a new .tpr file from an .mdp file with suitable energygrps. Use mdrun
-rerun to recalculate
Hi justin,
thank you for reply.
With best wishes and regards
Rama david.
On Fri, Oct 5, 2012 at 4:07 PM, Justin Lemkul jalem...@vt.edu wrote:
On 10/5/12 6:15 AM, rama david wrote:
Hi justin,
I completed the simulation ,
Now I want to use the selected residues of protein and ligand.
On 10/5/12 10:16 AM, rama david wrote:
Hi gromacs friends,
I completed the simulation of receptor and ligand,
I visualized the trajectory in the vmd I found most of the time C terminal
(ARG) interact with receptor ( 320 ASP) .
I want to find out these interaction energy between these two
Thank you for your Help.
I did the following tc-groups
tcoupl= V-rescale; modified Berendsen thermostat
tc-grps= extra34 Non-Protein energy; two coupling groups -
more accurate
tau_t= 0.10.1 0.1; time constant, in ps
ref_t= 310310 310
On 10/5/12 11:46 AM, rama david wrote:
Thank you for your Help.
I did the following tc-groups
tcoupl= V-rescale; modified Berendsen thermostat
tc-grps= extra34 Non-Protein energy; two coupling groups -
more accurate
tau_t= 0.10.1 0.1; time
Hi justin,
Ok now I get
I have to modify mdp parameter ..
Thank you,
With best wishes and regards,
Rama david
On Fri, Oct 5, 2012 at 9:47 PM, Justin Lemkul jalem...@vt.edu wrote:
On 10/5/12 11:46 AM, rama david wrote:
Thank you for your Help.
I did the following tc-groups
tcoupl
Hi,
I got the result by g_energy.
Thank you for these .
but when I used g_enemat with the edr file ( out put from mdrun -rerun )
g_enemat -f ener.edr -groups groups.dat
i got following out put
roup 0WARNING! could not find group (null):extra34-extra34 (0,0)in energy
file
WARNING! could not find
On 10/5/12 1:26 PM, rama david wrote:
Hi,
I got the result by g_energy.
Thank you for these .
but when I used g_enemat with the edr file ( out put from mdrun -rerun )
g_enemat -f ener.edr -groups groups.dat
i got following out put
roup 0WARNING! could not find group (null):extra34-extra34
On Mon, Oct 17, 2011 at 6:02 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Steven Neumann wrote:
Dear Gmx Users,
I would like to calculate the interaction energy (LJ and electrostatic)
between each residue and my ligands (10 ligands in the system). I would like
to see what is the
Steven Neumann wrote:
On Mon, Oct 17, 2011 at 6:02 PM, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu wrote:
Steven Neumann wrote:
Dear Gmx Users,
I would like to calculate the interaction energy (LJ and
electrostatic) between each residue and my
On Tue, Oct 18, 2011 at 11:41 AM, Justin A. Lemkul jalem...@vt.edu wrote:
Steven Neumann wrote:
On Mon, Oct 17, 2011 at 6:02 PM, Justin A. Lemkul jalem...@vt.edumailto:
jalem...@vt.edu wrote:
Steven Neumann wrote:
Dear Gmx Users,
I would like to calculate the
Steven Neumann wrote:
On Tue, Oct 18, 2011 at 11:41 AM, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu wrote:
Steven Neumann wrote:
On Mon, Oct 17, 2011 at 6:02 PM, Justin A. Lemkul
jalem...@vt.edu mailto:jalem...@vt.edu
mailto:jalem...@vt.edu
Dear Gmx Users,
I would like to calculate the interaction energy (LJ and
electrostatic) between each residue and my ligands (10 ligands in the
system). I would like to see what is the contribution of electrostatic and
vdW interactions between ligand and each of my residue. I thought to use
Steven Neumann wrote:
Dear Gmx Users,
I would like to calculate the interaction energy (LJ and
electrostatic) between each residue and my ligands (10 ligands in the
system). I would like to see what is the contribution of electrostatic
and vdW interactions between ligand and each of my
Dear Users !
Now i am able to do the protein solvent interaction !
thanks ! i have understood !
when i used the energygrps ,
when i used the
g_energy -f em.edr
this command it prints all terms and asks to make selection as below,
1 Bond 2 Angle3 Proper-Dih.
balaji nagarajan wrote:
Dear Users !
Now i am able to do the protein solvent interaction !
thanks ! i have understood !
when i used the energygrps ,
when i used the
g_energy -f em.edr
this command it prints all terms and asks to make selection as below,
1 Bond 2 Angle
Dear Users !
i would like to do this to a set of files !
so how to print the required values in the text mode or is there any flag for
this in
g_energy ,
thanks in advance
Date: Fri, 1 Jul 2011 13:40:28 -0400
From: jalem...@vt.edu
To: gmx-users@gromacs.org
Subject: Re: [gmx-users
the potential energy to an .xvg file, type:
11 0
and hit Enter. The values will be printed.
-Justin
g_energy ,
thanks in advance
Date: Fri, 1 Jul 2011 13:40:28 -0400
From: jalem...@vt.edu
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] interaction energy
balaji nagarajan wrote
: [gmx-users] interaction energy
balaji nagarajan wrote:
Dear Users !
Now i am able to do the protein solvent interaction !
thanks ! i have understood !
when i used the energygrps ,
when i used the
g_energy -f em.edr
this command
: Fri, 1 Jul 2011 13:53:59 -0400
From: jalem...@vt.edu
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] interaction energy
balaji nagarajan wrote:
Dear Users !
i would like to do this to a set of files !
so how to print the required values in the text mode
Dear all,
I have simulated a small peptide (+2 charge at pH=7) in water. Then i
calculate the interaction energy using energy_grps = Protein
SOL. The value of different energy terms are as
follows:
Hi
I want to obtain interaction energy between protein and dna in simulation
pr-dna complex.
what command is suitable for that?
Any help will highly appreciated!
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sandeep somani wrote:
i see. i reran the trajectory with reaction field electrostatics and
that gave a more negative energy value which was closer to what i was
expecting.
i guess the missing reciprocal space contributions explains this
discrepancy.
is there a way to get the full
i see. i reran the trajectory with reaction field electrostatics and that
gave a more negative energy value which was closer to what i was expecting.
i guess the missing reciprocal space contributions explains this
discrepancy.
is there a way to get the full interaction energy with PME ?
thnx
Hi All
I simulated a cubic box of 2180 TIP3P water molecules using gmx 3.3 and PME
for 400 ps and extracted the interaction energy of a randomly picked water
molecule with rest of the system.
Simulation was done at 298K and 1bar and usual procedure for generating a
water box and equilibration
Hi All
I simulated a cubic box of 2180 TIP3P water molecules using gmx 3.3 and PME
for 400 ps and extracted the interaction energy of a randomly picked
water
molecule with rest of the system.
Simulation was done at 298K and 1bar and usual procedure for generating
a
water box and
Rui Li wrote:
Hello!
Can I estimate the inhibit capability by interaction energy between the ligand
and protein?
Only about as well as you can estimate the results of a Formula One
racing season from the marks the drivers got on their drivers license exams.
And how can I get the
Hi all,
I want to calculate interaction energy between my ligand and residues of
proetins which come within 6A of any atoms of the raidus. I have defined
those residues and ligand as different groups. But how to select water
around 6A radius of the ligand during dynamicsfor the calculation. If I
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