am
Subject: Re: [gmx-users] Adsorption energy of a single molecule
To: Discussion list for GROMACS users
Message-ID: <4afb4be0.1020...@anu.edu.au>
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Darrell Koskinen wrote:
Hi Justin,
So when I create the index file with the mole
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
Subject: Re: [gmx-users] Adsorption energy of a single molecule
Date: Sun, 01 Nov 2009 19:29:36 -0500
From: "Justin A. Lemkul"
Subject: Re: [gmx-users] Adsorption energy of a single molecule
To: Discussion list for GROMACS users
Message-ID: <4aee27f0.50...@vt.edu>
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Darrell Koskine
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 adso
009 19:29:36 -0500
From: "Justin A. Lemkul"
Subject: Re: [gmx-users] Adsorption energy of a single molecule
To: Discussion list for GROMACS users
Message-ID: <4aee27f0.50...@vt.edu>
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Darrell Koskinen wrote:
Hi
performed.
-Justin
Thanks.
Darrell
***
***
Date: Sun, 01 Nov 2009 19:29:36 -0500
From: "Justin A. Lemkul"
Subject: Re: [gmx-users] Adsorption energy of a single molecule
To: Discussion list for GROMACS users
Message-ID: <4aee27f0.50...
hat adsorb on the second MD run?
Thanks.
Darrell
***
***
Date: Sun, 01 Nov 2009 19:29:36 -0500
From: "Justin A. Lemkul"
Subject: Re: [gmx-users] Ads
t to allow you to observe absorption events
from the individual energy profiles over time.
Mark
Date: Sun, 01 Nov 2009 07:17:24 -0500
From: "Justin A. Lemkul"
Subject: Re: [gmx-users] Adsorption energy of a single molecule
To: Discussion list for GROMACS users
Message-ID: <4aed7c54.20
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 sim
n mdtraj.trr -s mdtopol.tpr", 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"
Subject: Re: [gmx-users] Adsorption
use mdrun -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"
Subject: Re: [gmx-users] Adsorption energy of a single molecule
To: Discuss
-0400
From: "Justin A. Lemkul"
Subject: Re: [gmx-users] Adsorption energy of a single molecule
To: Discussion list for GROMACS users
Message-ID: <4ae9d9a3.9080...@vt.edu>
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darre...@ece.ubc.ca wrote:
Dear GROMACS Gurus,
I
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 t
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 sing
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