g_sham calculates free energy landscapes by computing the joint
probability distribution from the two dimensional plane constructed
using two quantities (in your case it will be rmsd and radius of
gyration). Conformations sampled during the simulation were projected
on this two dimensional plane,
Thank you Sir
Regards
kavya
On Sun, Mar 31, 2013 at 11:58 AM, bipin singh bipinel...@gmail.com wrote:
g_sham calculates free energy landscapes by computing the joint
probability distribution from the two dimensional plane constructed
using two quantities (in your case it will be rmsd and
I have polymer and clay structures and I need to study their surface
interaction. How do I keep a clay box on top of polymer.
Thanks in advance.
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On 2013-03-31 12:21, Kavyashree M wrote:
Thank you Sir
Note that the free energy differences are rigorously correct only if the
array of the cells in the grid correspond units of phase space with the
same volume. This is close to impossible to achieve, but the plots may
still give insight.
On 3/31/13 6:38 AM, Abhinav Agrawal wrote:
I have polymer and clay structures and I need to study their surface
interaction. How do I keep a clay box on top of polymer.
The concepts of top and bottom are irrelevant in a periodic system. You can
position anything within the unit cell
Hi,
To inactivate a position restraint, is it enough to make the define command in
mdp file to a comment?
;define= DPOSRES
Sincerely,
Shima
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On 3/31/13 8:16 AM, Shima Arasteh wrote:
Hi,
To inactivate a position restraint, is it enough to make the define command in
mdp file to a comment?
;define= DPOSRES
Yes. Or remove it altogether.
-Justin
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Justin A. Lemkul, Ph.D.
Research
Dear all,
In order to get density profile of a pure system the box has to get
extended in one drection (e.g Z) as we do for surface tension calculations
or density profile
can be also obtained from the usual box filled up with the molecules
without need for empty space in Z
Thanks for any
On 3/31/13 11:41 AM, Elisabeth wrote:
Dear all,
In order to get density profile of a pure system the box has to get
extended in one drection (e.g Z) as we do for surface tension calculations
or density profile
can be also obtained from the usual box filled up with the molecules
without need
Dear gmx users,
Does anyone know how to obtain structure file for the simple ethylene
molecule ( C-C) ? I tried PRODRG but it fails to generate structure files
for di atomic molecules.
Any suggestion is appreciated!
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Thanks,
J. N.
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On 3/31/13 12:23 PM, Juliette N. wrote:
Dear gmx users,
Does anyone know how to obtain structure file for the simple ethylene
molecule ( C-C) ? I tried PRODRG but it fails to generate structure files
for di atomic molecules.
Any suggestion is appreciated!
For something as simple as a
Thank Justin. I am interested in the density profile at the solvent-air
interface. I wanted to see how density changes with position at different
pressures...I have the equilibrated boxes at several pressures obtained
from NPT but I am not sure whether running g_density on the current
simulations
On 3/31/13 12:27 PM, Elisabeth wrote:
Thank Justin. I am interested in the density profile at the solvent-air
interface. I wanted to see how density changes with position at different
pressures...I have the equilibrated boxes at several pressures obtained
from NPT but I am not sure whether
Thanks Justin for your reply. To avoid compressing down the cell I thought
using semiisotropic option with 0 compressibility in Z would be
appropriate.
Here are the steps:
1- First I did a 10 ns NPT to equilibrate the box and used the last frame
gro and cpt file as input for the next step
2- I
On 3/31/13 1:12 PM, Elisabeth wrote:
Thanks Justin for your reply. To avoid compressing down the cell I thought
using semiisotropic option with 0 compressibility in Z would be
appropriate.
Here are the steps:
1- First I did a 10 ns NPT to equilibrate the box and used the last frame
gro and
Thanks Justin for your reply. To avoid compressing down the cell I thought
using semiisotropic option with 0 compressibility in Z would be
appropriate.
You must use NVT only. Otherwise, the cell will compress in XY directions
to compensate its inability to compress in Z direction.
Here
Actually my doubt was how to make a simulation box from two structure files
i.e. how do i keep the clay and poymer boxes close to each other to run
energy minimization
Message: 4
Date: Sun, 31 Mar 2013 07:38:38 -0400
From: Justin Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] Making
On 3/31/13 2:22 PM, Abhinav Agrawal wrote:
Actually my doubt was how to make a simulation box from two structure files
i.e. how do i keep the clay and poymer boxes close to each other to run
energy minimization
Consider the following:
Thanks Vitaly. I am wondering what is the use of semiisotropic with 0
compressibility in Z then? I was hoping to run NPT to secure a fixed
pressure.
I also wanted to know if surface tension can be also calculated under NVT
(if NPT fails for this puporse)
Thanks!
On 31 March 2013 14:01, Dr.
Hi Elisabeth -
On Sun, Mar 31, 2013 at 8:28 PM, Elisabeth katesed...@gmail.com wrote:
Thanks Vitaly. I am wondering what is the use of semiisotropic with 0
compressibility in Z then? I was hoping to run NPT to secure a fixed
pressure.
Please, read about Gibbs phase rule... This is your
Dear All -
Does Gromacs possess a convenient utility to [randomly] substitute solvent
particles by given number of multiatomic solutes?
Dr. Vitaly Chaban
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On 3/31/13 4:26 PM, Dr. Vitaly Chaban wrote:
Dear All -
Does Gromacs possess a convenient utility to [randomly] substitute solvent
particles by given number of multiatomic solutes?
No, but you can easily add the number of solutes you need with genbox -ci -nmol
and then solvate afterwards.
Yes, I can
Could you briefly explain the difference between -cp and -cs options?
On Sun, Mar 31, 2013 at 10:34 PM, Justin Lemkul jalem...@vt.edu wrote:
On 3/31/13 4:26 PM, Dr. Vitaly Chaban wrote:
Dear All -
Does Gromacs possess a convenient utility to [randomly] substitute solvent
On 3/31/13 5:02 PM, Dr. Vitaly Chaban wrote:
Yes, I can
Could you briefly explain the difference between -cp and -cs options?
From genbox -h:
Specify -cp (solute) and -cs (solvent).
-Justin
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Justin A. Lemkul, Ph.D.
Research Scientist
Hi All,
I'm trying to cluster a pdb trajectory format file and I'm getting odd
results. The command line i'm using is:
g_cluster -f 0to7.pdb -s cysTerm.pdb -g cluster.log -o rmsd-clust.xpm -dist
rmsd-dist.xvg -cl clusters.pdb -method monte-carlo -seed 4540 -niter 1
And everything seems to
Hi everyone,
I am trying to insert two same proteins in a simulation box. Now I have
used pdb2gmx to convert one protein's pdb file to gro file. Then how should
I do? How could they be randomly positioned and oriented in the box?
Thanks in advance.
Zhikun
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On 3/31/13 9:51 PM, Zhikun Cai wrote:
Hi everyone,
I am trying to insert two same proteins in a simulation box. Now I have
used pdb2gmx to convert one protein's pdb file to gro file. Then how should
I do? How could they be randomly positioned and oriented in the box?
Place them however you
Dear Prof Mobley,
I have some additional questions in understanding the free energy
calculations.
1) When doing a mutation from a larger aminoacid to a smaller one, one
necessarily ends up with dummy atoms and atoms that have different mass. In
my case when the glutamate is converted into a
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