I came across one such application name PLUMED plugin for gromacs, for
dihedral restraints as the reaction coordinate.
If you can suggest any other application for the same, kindly let me know.
--Thanks
Neeru
> On 4/15/13 2:27 AM, neeru sharma wrote:
> > Dear gromacs users,
> >
Dear gromacs users,
I want to calculate PMF using pull code in gromacs, taking a psi angle as
the reaction coordinate.
I have a doubt where it is possible with the geometry options, currently
available in gromacs?
Thanks and regards
Neeru
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http
flowed
>
>
>
> On 3/21/13 4:29 AM, neeru sharma wrote:
> >> Message: 6
> >> Date: Wed, 20 Mar 2013 09:04:05 -0400
> >> From: Justin Lemkul
> >> Subject: Re: [gmx-users] Restraining water molecule
> >> To: Discussion list for GROMACS users
gt;
> Content-Type: text/plain; charset=ISO-8859-1
>
> On Wed, Mar 20, 2013 at 8:57 AM, neeru sharma >wrote:
>
> > Dear gromacs users,
> >
> > I am simulating a system of Protein-ion-GTP with One Water molecule. I
> want
> > to restrain this system
Dear gromacs users,
I am simulating a system of Protein-ion-GTP with One Water molecule. I want
to restrain this system (along with this water molecule) for minimization
and equilibration.
Everytime I run this by specifying the .itp files, it gives the error of
misplacement as follows:
*"This pr
>
> On 2/12/13 1:12 AM, neeru sharma wrote:
> > Dear Gromacs Users,
> >
> >
> > I have simulated a system of protein-ion complex. As a part of the
> > analysis, I want to see whether there are any H-bonds or other
> interactions
> > between the active
Thanks Stephan for you suggestion.
I will try the analysis with larger value of bins.
--Neeru
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--
gmx-users mai
Thanks Justin for your reply.
I did see that the default bins value is 200, but I was not sure what does
it signify. It says " no of bins used in the analysis".
That's why I was confused whether it is equal to no. of umbrella sampling
simulations we run and give input to g_wham.
Thanks for cleari
:
1) Should I use more than 15 bins in my case, and the one that gives
proper overlap in histogram ?
2) Or any number of bins (even if it is less than 12) can be used, if
I get proper overlap in my histogram output?
Any suggestion is appreciated.
--
Thanks and regards,
Neeru Sharma
--
gmx-users
:
1) Should I use more than 15 bins in my case, and the one that gives
proper overlap in histogram ?
2) Or any number of bins (even if it is less than 12) can be used, if
I get proper overlap in my histogram output?
Any suggestion is appreciated.
--
Thanks and regards,
Neeru Sharma
--
gmx-users
Thanks Justin for all your comments and suggestion.
I am not using any position restraints as of now.
But I will try out more parameters and more options. Thanks again.
--Neeru
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View this message in context:
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Dear Justin,
Thanks for the suggestion regarding the pull force.
1)I will try by reducing the pull force to 1000 and 100 KJmol/nm2 now.
Regarding the force being applied in z-direction, after visualizing my
trajectory i thought it would work by providing force in z-direction.
2)Regarding the pro
Dear Stephan,
Actually I had less idea about the force parameters of the pulling
simulation, that's why I started with this force. I will again retry by
reducing the force to 1000 and 100 KJmol/nm-2 too. Any suggestion regarding
the other parameters is also welcome!!
Thanks for your response!!
-
Dear Thomas,
Thanks for ur reply. I have visualized my trajectory and found no water
molecule in between. Moreover, there are no residues in between the
"Residue" and GTP molecule too. I feel I have already applied a large force
for the pulling. Still I will consider you suggestion.
One query rega
000
also. In both of the case, the trajectories showed the distance
stabilized near _4.25 A only.
Can anyone please tell me the reason behind it? What should I do, so
that I could get the desired distance ?
Any suggestion and help is welcome !!!
Thanks,
Neeru Sharma
--
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000
also. In both of the case, the trajectories showed the distance
stabilized near _4.25 A only.
Can anyone please tell me the reason behind it? What should I do, so
that I could get the desired distance ?
Any suggestion and help is welcome !!!
Thanks,
Neeru Sharma
--
gmx-users mailing list
Thanks Justin for your early response. I was confused about it, but
now it's clear. Thanks
--Neeru
> Dear Gromacs Users,
>
>
> I have some queries about the parameters in the .mdp file for the pull code.
>
> If I want to pull my ligand, towards specific atom/group of atoms from
> the protein, how
Dear Gromacs Users,
I have some queries about the parameters in the .mdp file for the pull code.
If I want to pull my ligand, towards specific atom/group of atoms from
the protein, how am I supposed to mentioned these in the mdp file?
calculate some kind of energy barrier
or PMF needed to form these 2 H-bonds along the simulation length?
Any suggestion is welcome.
Thanks,
Neeru
Dear Neeru Sharma,
I know off hand from years of work with Mg-GTP sites, they are
realativly rigid/staritforward. If the bonds arn't present
Dear Christopher Neale,
Let me re-frame my question again.
Though I am new to US, but I have a basic idea about performing US. My
main query lies for these 2 H-bonds: one between Protein and MG and
other one between protein and GTP.
I want to know if I can perform umbrella sampling to explain th
Dear Gromacs Users,
I am simulating a system containing Protein-Mg-GTP complex.
I intend to perform the umbrella sampling on the system to calculate
PMF and to perform wham analysis.
I have generated a series of conformations for the umbrella sampling.
My main consideration is towards the 2 H-bon
plain; charset=ISO-8859-1; format=flowed
>
>
>
> On 6/7/12 8:26 AM, neeru sharma wrote:
> > Dear Justin,
> >
> > Greetings of the day!!
> >
> > I am following your tutorial for the calculation of free energy change
> in gromacs.
> >
> > It says a
system?
For example, I have a Protein-Mg-GTP complex (In initial state A, 2
specific H-bonds are absent and in the final state, these 2 H-bonds are
present). So, how can I implement this for the calculation of change in
free energy to my system?
Thanks and Regards,
Neeru Sharma
CDAC, Pune
was crossed to reach state 2 (2
H-bonds) from state 1. Can you suggest me some way to find this energy
barrier in gromacs ?
Thanks in anticipation.
--
Regards,
Neeru Sharma
Project Engineer,
Molecular Modelling Team, Bioinformatics Group,
Centre for Development of Advanced Computing (CDAC
Dear gromacs users,
I am running steered MD simulation using Plumed plugin in gromacs for a
system consisting of Protein-Mg-GTP complex. I have to calculate the
distance of specific atoms with Mg and GTP.
While visualizing the trajectories using vmd, I am encountering some
problems.
1) While usi
Dear gromacs users,
I am a gromacs user and need some help regarding the implementation of
PLUMED plugin in gromacs.
I am simulating a system containing Protein-Mg-GDP and Protein-Mg-GTP using
Gromacs which is a 166 residue protein+mg+GTP/GDP complex. I have already
carried out classical MD simul
place to start, since you have initial and
> final structures.
>
> To my knowledge, none of these is implemented directly within GROMACS,
> but all could be implemented using GROMACS as a dynamics backend.
> (NEB
>
> On Wed, Apr 18, 2012 at 2:26 AM, neeru sharma
>
for Eflnull, tau and deltaFO in flooding
for a protein system ?
As, I am new to gromacs, can you please help me regarding the above
mentioned matter and how it can be approached with my system?
Any help will be highly appreciated.
Regards,
Neeru Sharma
--
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appreciated.
Thanks in advance
-
Neeru Sharma,
Pune (India)
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this
situation?
If anyone has simulated any similar system with Protein-ion-ligand complex
or have faced similar problem, please share with what to do now to resolve
this issue or to simulation such a system?
Any help will be highly appreciated.
Thanks
-
Neeru Sharma,
Pune (India)
--
gmx-
Thanks Justin.
I have tried both ways now and considering Protein_MG_GDP and Water_ions
groups, it is running without any error but Protein_GDP and MG_Water_ions
is failing with an error message.
Thanks again...
Neeru
>
> neeru sharma wrote:
> >
> >
> > Thanks Jus
Thanks Justin.
I tried the simulation with Protein_GDP and Water_ions, considering that
"Water_and_ions" group will include MG. But it didn't work showing an
error,saying "One atom not present in the coupling group". Shall I try to
include MG in Water_ions group via make_
is on
tcoupl = V-rescale
tc-grps = Protein_MG_GDP Water_and_ions
Is this coupling method correct, to treat Protein and Mg as different
quantities?
Thanks
---
Neeru Sharma
Pune (India)
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in AMBER03 too?
Neeru
>
> On 10/12/2011 6:25 AM, neeru sharma wrote:
> > Dear gromacs users,
> >
> > I have to simulate a protein-GDP complex using gromacs.As PRODRG was
> > giving unreliable output, I generated Amber topology and coordinate
> > files for GTP m
the
antechamber command itself. OR if anybody has the paramters or topology for
GDP, can anyone provide me the same so that I can compare and see where the
parameters are differing.
Thanks
Neeru Sharma
Pune (India)
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other tool to do so.
Thanks
Neeru Sharma
CDAC, Pune (India)
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