Dear all,
I have found density of states (Dos) of a protein ligand system from gmx dos
command of gromacs. I would like to know if it employs the same principle
component analysis as used in g_covar. If not what are the differences.
Also the Dos obtained from gmx dos has solid and diffusive
Dear all,
I have to find vibrational spectrum of a protein-ligand complex in water using
MD. Can anyone please suggest me what thermostats would be suited for NVT
equilibration, NPT equilibration and MD production. I have read that for NVT,
berendsen is suited while for NPT and MD part,
Dear all,
I am attempting to find the Vibrational density of states of protein bound to
ligand in a water box using the command g_dos. To do so, should I extract the
protein part from the entire trajectory file containing coordinates and
velocities of all atoms (trr file) and then run g_dos on
Dear Justin,
I used the following command to print ascii format of the hessian matrix to a
file from the default mtx format of gromacs obtained after normal mode analysis.
gmxdump_d -mtx nm.mtx > hessian_matrix.dat
I would like to confirm the way the hessian matrix is written in this new ascii
Dear all,
I used the following command to print ascii format of the hessian matrix to a
file from the default mtx format of gromacs obtained after normal mode analysis.
gmxdump_d -mtx nm.mtx > hessian_matrix.dat
I would like to confirm the way the hessian matrix is written in this new ascii
Dear Justin,
To get an estimate of the long range interactions in LIE calculations for
protein-ligand binding energy calculations, is it reasonable to change the
coulomb type to reaction-field zero instead of changing the rcoulomb from 1.0
nanometre to half of the water box, and the
Dear all,
I used the following command to print ascii format of the hessian matrix to a
file from the default mtx format of gromacs obtained after normal mode analysis.
gmxdump_d -mtx nm.mtx > hessian_matrix.dat
I would like to confirm the way the hessian matrix is written in this new ascii
Dear Justin,
I used the following command to print ascii format of the hessian matrix to a
file from the default mtx format of gromacs obtained after normal mode analysis.
gmxdump_d -mtx nm.mtx > hessian_matrix.dat
I would like to confirm the way the hessian matrix is written in this new ascii
Dear Justin,
I attempted to write the energy file (edr file) after performing normal mode
analysis (using integrator = nm), but couldn't find gromacs writing nm.edr file
at the end of the nm analysis similar to the way it writes em.edr after energy
minimization. So firstly, is it plausible to
as evolved into a
distorted one?
Is there any other way where I can avoid the said warning other than increasing
table-extension and maintaining couple-intramol = no in my minimizing code with
the free energy addendum.
Thank you,
Bhagyesh
- Original Message -----
From: "Varvdekar Bh
rg
Sent: Thursday, June 29, 2017 6:48:25 PM
Subject: Re: [gmx-users] Doubt about Free Energy control Minimization
On 6/29/17 5:11 AM, Varvdekar Bhagyesh Rajendra wrote:
> Dear Justin,
>
> I am getting the same following warning even after minimizing the system
> twice using cg integra
ers] Doubt about Free Energy control Minimization
On 6/27/17 7:43 AM, Varvdekar Bhagyesh Rajendra wrote:
> Dear Justin,
>
> When the system is minimized with full interactions with no free energy code,
> I see no warnings and the systems is minimized properly.
>
> However, w
Tuesday, June 27, 2017 6:42:33 PM
Subject: Re: [gmx-users] Doubt about Free Energy control Minimization
On 6/26/17 9:09 AM, Varvdekar Bhagyesh Rajendra wrote:
> Dear Justin,
>
> I have encountered the following warning when I used the following code to
> minimize my protein-ligand
t;Justin Lemkul" <jalem...@vt.edu>
To: gmx-us...@gromacs.org
Sent: Wednesday, June 14, 2017 4:50:58 AM
Subject: Re: [gmx-users] Doubt about Free Energy control Minimization
On 6/13/17 4:31 PM, Varvdekar Bhagyesh Rajendra wrote:
> Dear Justin,
>
> I aspire to derive energy-mini
;jalem...@vt.edu>
To: gmx-us...@gromacs.org
Sent: Wednesday, June 14, 2017 4:50:58 AM
Subject: Re: [gmx-users] Doubt about Free Energy control Minimization
On 6/13/17 4:31 PM, Varvdekar Bhagyesh Rajendra wrote:
> Dear Justin,
>
> I aspire to derive energy-minimum structures when the int
Dear Justin,
I aspire to derive energy-minimum structures when the interaction potential
energy between the protein and the ligand are multiplied by 0.9, 0.8, 0.7,...,
0.2, 0.1.
I presume the following Free Energy minimization code mentioned in gromacs
tutorial may do the trick. I would
Dear Justin,
I have used PME in the production runs of my systems for finding Delta
G_Binding using g_lie. But many threads on Gromacs forum warn against it and
advise to rerun the whole trajectory using Reaction field Zero, but the cutoff
for this rerun is not clearly given. Some threads say
ustin Lemkul" <jalem...@vt.edu>
To: gmx-us...@gromacs.org
Sent: Tuesday, June 13, 2017 2:18:30 AM
Subject: Re: [gmx-users] Doubt about Free Energy Calculations using g_bar
On 6/12/17 11:47 AM, Varvdekar Bhagyesh Rajendra wrote:
> Dear Justin,
>
> I have compiled the following
in anticipation,
Best Regards,
Bhagyesh
- Original Message -
From: "Justin Lemkul" <jalem...@vt.edu>
To: gmx-us...@gromacs.org
Sent: Sunday, June 11, 2017 7:01:26 AM
Subject: Re: [gmx-users] Doubt about Free Energy Calculations using g_bar
On 6/10/17 6:15 AM, Varvdekar Bhagyes
st Regards,
Bhagyesh
- Original Message -
From: "Mark Abraham" <mark.j.abra...@gmail.com>
To: gmx-us...@gromacs.org
Sent: Monday, June 12, 2017 2:43:53 AM
Subject: Re: [gmx-users] Doubt about Free Energy Calculations using g_bar
Hi,
On Sun, Jun 11, 2017 at 10:39 PM V
gromacs.org
Sent: Sunday, June 11, 2017 9:22:51 PM
Subject: Re: [gmx-users] Doubt about Free Energy Calculations using g_bar
Hi,
To what end? These are non-physical states.
Mark
On Sun, 11 Jun 2017 16:28 Varvdekar Bhagyesh Rajendra <
bhagyesh.varvde...@research.iiit.ac.in> wrote:
> D
une 11, 2017 7:01:26 AM
Subject: Re: [gmx-users] Doubt about Free Energy Calculations using g_bar
On 6/10/17 6:15 AM, Varvdekar Bhagyesh Rajendra wrote:
> Dear Justin,
>
> Just so we are on the same page, this means that if I don't touch the
> topology file and use the following m
emkul" <jalem...@vt.edu>
To: gmx-us...@gromacs.org
Sent: Saturday, June 10, 2017 5:12:25 AM
Subject: Re: [gmx-users] Doubt about Free Energy Calculations using g_bar
On 6/8/17 6:14 PM, Varvdekar Bhagyesh Rajendra wrote:
> Dear Justin,
>
> I was interested in the process *prior*
u>
To: gmx-us...@gromacs.org
Sent: Friday, June 9, 2017 2:40:38 AM
Subject: Re: [gmx-users] Doubt about Free Energy Calculations using g_bar
On 6/8/17 11:46 AM, Varvdekar Bhagyesh Rajendra wrote:
> Dear all,
>
> I am attempting to find Binding affinity of a Protein-ligand system by
> followi
Dear all,
I am attempting to find Binding affinity of a Protein-ligand system by
following the Free Energy tutorials
(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html).
It says : "The procedure in this tutorial essentially assumes that charges have
Dear all,
Is there any way of scaling the Coulombic and/or van der Waals interactions
between a protein-ligand system and simultaneously doing Normal Mode analysis
on the perturbed system while scaling, perhaps using free-energy code in
Gromacs?
Thanking in anticipation,
Best Regards,
affinity calculations?
Best Regards,
Bhagyesh
- Original Message -
From: "Justin Lemkul" <jalem...@vt.edu>
To: gmx-us...@gromacs.org
Sent: Friday, June 2, 2017 4:10:21 PM
Subject: Re: [gmx-users] Doubt about gmx wham analysis
On 6/1/17 6:29 PM, Varvdekar Bhagyesh Rajendra wrot
: "Varvdekar Bhagyesh Rajendra" <bhagyesh.varvde...@research.iiit.ac.in>
To: gmx-us...@gromacs.org
Sent: Thursday, June 1, 2017 7:35:16 PM
Subject: Re: [gmx-users] Doubt about gmx wham analysis
Dear Justin,
Gazillion thanks for the valuable insight!
Best Regards,
Bhagyesh
-
5/31/17 10:49 AM, Varvdekar Bhagyesh Rajendra wrote:
> Dear Justin,
>
> During the pulling part of the umbrella sampling for finding binding affinity
> of the Protien-ligand system, the ligand(peptide) is deformed and its helices
> straighten along with large conformational c
Regards,
Bhagyesh
- Original Message -
From: "Varvdekar Bhagyesh Rajendra" <bhagyesh.varvde...@research.iiit.ac.in>
To: gmx-us...@gromacs.org
Sent: Wednesday, May 31, 2017 6:42:41 PM
Subject: Re: [gmx-users] Doubt about gmx wham analysis
Dear Justin,
Many Thanks for
t about gmx wham analysis
On 5/31/17 8:34 AM, Varvdekar Bhagyesh Rajendra wrote:
> Dear Justin,
>
> In my Protein-ligand system, I have used pull_coord1_dim = Y Y Y and the
> ligand is pulled along the COM of two groups protein-ligand in all directions
> to calculate binding a
u>
To: gmx-us...@gromacs.org
Sent: Wednesday, May 31, 2017 5:42:52 AM
Subject: Re: [gmx-users] Doubt about gmx wham analysis
On 5/30/17 6:49 AM, Varvdekar Bhagyesh Rajendra wrote:
> Dear all,
>
> I have followed the Umbrella sampling tutorial
> (http://www.bevanlab.biochem.vt.
Dear all,
Is it possible to do constrained Normal Mode Analysis in Gromacs such as a free
ligand buried in a constrained protein to study the effects of the binding on
the normal modes of ligand? I had tried to used DPOSRES_A, as my protein is
chain A, but everytime gromacs throws the error
Dear all,
I have followed the Umbrella sampling tutorial
(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html)
on a Protein-ligand system using gromacs 5.1.1 while making some changes in
md_pull code with pull_coord1_dim = Y Y Y . Now I have to perform
2017 7:25:43 PM
Subject: Re: [gmx-users] Doubts about g_lie and g_bar
Hi,
On Sat, May 13, 2017 at 5:18 PM Varvdekar Bhagyesh Rajendra <
bhagyesh.varvde...@research.iiit.ac.in> wrote:
> Dear all,
>
> I have tried to find Delta G of Binding using g_lie and g_bar from the
> following s
Dear all,
I have tried to find Delta G of Binding using g_lie and g_bar from the
following systems (Protein+Ligand with ligand = chain B):
PDB Ids: 1CDL, 1CKK, 1NIW, 2L7L, 2o60.
I have encountered following 2 doubts while doing so:
1. This doubt may have been answered in the past threads but I
Dear all,
I have tried to find Delta G of Binding using g_lie and g_bar from the
following systems (Protein+Ligand with ligand = chain B):
PDB Ids: 1CDL, 1CKK, 1NIW, 2L7L, 2o60.
I have encountered following 2 doubts while doing so:
1. This doubt may have been answered in the past threads but I
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