I'm working with a protein in water and I used periodic boundary conditions
in three dimension.
At first the initial system was minimized, then I followed Justin's
protocol. The system was equilibrated in a first stage nvt for 1 ns and in a
second stage npt for 1 ns (with restraints).
Then the
On 2/6/13 11:56 AM, Yara Alves wrote:
I'm working with a protein in water and I used periodic boundary conditions
in three dimension.
At first the initial system was minimized, then I followed Justin's
protocol. The system was equilibrated in a first stage nvt for 1 ns and in a
second stage
On 27/12/12 16:29, vahid garshasbi wrote:
I run my simulation, now i want to analysis my data. i simulate ion
adsorption on CNT and i want to determine adsorption values in
deffrent concentrations of ion and then plot adsorpttion curve. what
shod i do?
Ask your advisor.
thanks, vahid
--
ammonia
molecule and the graphene sheet.
I am not aware that OPLS-AA was parameterized to produce such values,
but would appreciate your comments.
Thanks.
Darrell
Message: 2
Date: Thu, 12 Nov 2009 10:42:24 +1100
From: Mark Abraham mark.abra...@anu.edu.au
Subject: Re: [gmx-users] Adsorption
...@anu.edu.au
Subject: Re: [gmx-users] Adsorption energy of a single molecule
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID: 4afb4be0.1020...@anu.edu.au
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Darrell Koskinen wrote:
Hi Justin,
So when I create
A. Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] Adsorption energy of a single molecule
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID: 4aee27f0.50...@vt.edu
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Darrell Koskinen wrote:
Hi Justin,
In my
Darrell Koskinen wrote:
Hi Justin,
So when I create the index file with the molecule and the graphene sheet
and run g_energy, is the adsorption energy between the adsorbed molecule
and the graphene sheet the LJ (SR) energy? And will this energy be just
the interaction energy between the
Subject: Re: [gmx-users] Adsorption energy of a single molecule
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID: 4aee4387.40...@vt.edu
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Darrell Koskinen wrote:
Hi Justin,
Since I cannot use the original .tpr file
-rerun with your new .tpr file, and g_energy (not gmxdump) to
analyze the energies between the various groups.
-Justin
Thanks.
Darrell
Date: Thu, 29 Oct 2009 14:06:27 -0400
From: Justin A. Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] Adsorption energy of a single molecule
To: Discussion list
, where
mdtraj.trr and mdtopol.tpr are the output of the initial simulation, and
then use g_energy to analyze the energies between the groups?
Thanks.
Darrell
Date: Sun, 01 Nov 2009 07:17:24 -0500
From: Justin A. Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] Adsorption energy of a single
Darrell Koskinen wrote:
Hi Justin,
In my simulation, I have just over 100 ammonia molecules and, of these
molecules, 10 to 20 adsorb onto the graphene sheet. I initially thought
that I would need to tag each one of the ammonia molecules, since I
would not know, in advance of running the
absorption events
from the individual energy profiles over time.
Mark
Date: Sun, 01 Nov 2009 07:17:24 -0500
From: Justin A. Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] Adsorption energy of a single molecule
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID: 4aed7c54.2080
Dear GROMACS Gurus,
Is it possible to determine the adsorption energy of a single molecule in
a simulation? My simulation has a large number of gas phase molecules
distributed throughout a box with some molecules adsorbed on a graphene
sheet. I would like to compare the adsorption energy of a
darre...@ece.ubc.ca wrote:
Dear GROMACS Gurus,
Is it possible to determine the adsorption energy of a single molecule in
a simulation? My simulation has a large number of gas phase molecules
distributed throughout a box with some molecules adsorbed on a graphene
sheet. I would like to compare
Dear all I am mainly a scientist and I would like to complete my experimental
data with some software simulation.
Can Gromacs or model the adsorption and the nucleation of proteins on surfaces
or there is no technical feasibility for this Software on such a modeling?
Agnese Zicari wrote:
Dear all I am mainly a scientist and I would like to complete my
experimental data with some software simulation.
Can Gromacs or model the adsorption and the nucleation of proteins on
surfaces or there is no technical feasibility for this Software on
such a modeling?
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