Re: [gmx-users] Adsorption energy of a single molecule
Darrell Koskinen wrote: Hi Mark, No, I am not trying to build a random number generator and hope that I am not moving in this direction : ) My definition of adsorption energy would be the difference in energy when two species are at an infinite distance and the energy when these species are at an equilibrium distance from each other. OK, but I think you need to measure a free energy change, using (for example) a PMF generated by the pulling code in GROMACS. I think the way in which I can measure this energy difference would be to subtract the LJ (LR) energy between an ammonia molecule and the graphene sheet (where the distance between the molecule and the graphene sheet is large) from the LJ (SR) energy between an adsorbed ammonia molecule and the graphene sheet. That assumes an unrealistic independence of the forcefield contributions. Why would energy not partition over bonded and Coulombic interactions also? Also, the distinction between LR and SR is merely to do with your twin-range cut-off choices (read manual!). The adsorption process is a transition from no interaction (i.e. outside the LR cutoff) to physical contact. The total LJ interaction energy (if that means anything!) will be partitioned between LR and SR according to distance from the surface. I am not aware that OPLS-AA was parameterized to produce such values, but would appreciate your comments. I know nothing about OPLS-AA, but would guess that it wasn't parameterized for graphite, gaseous ammonia or to reproduce adsorption energies. I think you'd have to demonstrate (through simulation or literature reference) suitable behaviour of graphite and gaseous ammonia on their own before trying to simulate them together. If there's some kind of experimental observable about the behaviour of adsorbed ammonia on graphite that you could reproduce, that would be a useful indicator that the force field is doing OK. Absent that, you might just have that random number generator :-) Mark Message: 2 Date: Thu, 12 Nov 2009 10:42:24 +1100 From: Mark Abraham Subject: Re: [gmx-users] Adsorption energy of a single molecule To: Discussion list for GROMACS users Message-ID: <4afb4be0.1020...@anu.edu.au> Content-Type: text/plain; charset=ISO-8859-1; format=flowed 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? Not necessarily, unless the force field was parameterized to produce such values. First, seek to define what you mean by adsorption (free) energy, then consider how a simulation might measure that. Then, consider whether any force fields exist that might achieve that. Then, test it on a case where you have experimental data. Other procedures run a much higher risk of producing an expensive random number generator :-) And will this energy be just the interaction energy between the adsorbed molecule and the graphene sheet (i.e. does the creation of the new index file and executing -rerun cause g_energy to exclude the energies between the other molecules and the graphene sheet)? Creating an energy group causes mdrun -rerun to report the fraction of the total nonbonded energies that are due to intra- and inter-group interactions. See manual section 3.3 Mark Date: Sun, 01 Nov 2009 21:27:19 -0500 From: "Justin A. Lemkul" Subject: Re: [gmx-users] Adsorption energy of a single molecule To: Discussion list for GROMACS users Message-ID: <4aee4387.40...@vt.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Darrell Koskinen wrote: Hi Justin, Since I cannot use the original .tpr file, then do I need to run grompp with the new index file to create a "new" .tpr file, "mdtopolnew.tpr"? I assume I then need to modify the energygrps line within the .mdp file to include these new energy groups and then execute "mdrun -rerun mdtraj.trr -s mdtopolnew.tpr". Is this correct? Yes, that is the point of the -rerun function. Does executing "mdrun -rerun mdtraj.trr -s mdtopolnew.tpr" cause a molecular dynamics simulation to run once again? If so, then will the exact same molecules that adsorbed on the first MD run be the same ones that adsorb on the second MD run? The original coordinates are used to re-calculate the energies. No new simulation is 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...@vt.edu> Content-T
[gmx-users] Adsorption energy of a single molecule
Hi Mark,
No, I am not trying to build a random number generator and hope that I
am not moving in this direction : )
My definition of adsorption energy would be the difference in energy
when two species are at an infinite distance and the energy when these
species are at an equilibrium distance from each other.
I think the way in which I can measure this energy difference would be
to subtract the LJ (LR) energy between an ammonia molecule and the
graphene sheet (where the distance between the molecule and the graphene
sheet is large) from the LJ (SR) energy between an adsorbed 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
To: Discussion list for GROMACS users
Message-ID: <4afb4be0.1020...@anu.edu.au>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
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?
Not necessarily, unless the force field was parameterized to produce
such values. First, seek to define what you mean by adsorption (free)
energy, then consider how a simulation might measure that. Then,
consider whether any force fields exist that might achieve that. Then,
test it on a case where you have experimental data.
Other procedures run a much higher risk of producing an expensive random
number generator :-)
And will this energy be just
the interaction energy between the adsorbed molecule and the graphene
sheet (i.e. does the creation of the new index file and executing -rerun
cause g_energy to exclude the energies between the other molecules and
the graphene sheet)?
Creating an energy group causes mdrun -rerun to report the fraction of
the total nonbonded energies that are due to intra- and inter-group
interactions. See manual section 3.3
Mark
Date: Sun, 01 Nov 2009 21:27:19 -0500
From: "Justin A. Lemkul"
Subject: Re: [gmx-users] Adsorption energy of a single molecule
To: Discussion list for GROMACS users
Message-ID: <4aee4387.40...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Darrell Koskinen wrote:
Hi Justin,
Since I cannot use the original .tpr file, then do I need to run
grompp with the new index file to create a "new" .tpr file,
"mdtopolnew.tpr"? I assume I then need to modify the energygrps line
within the .mdp file to include these new energy groups and then
execute "mdrun -rerun mdtraj.trr -s mdtopolnew.tpr". Is this correct?
Yes, that is the point of the -rerun function.
Does executing "mdrun -rerun mdtraj.trr -s mdtopolnew.tpr" cause a
molecular dynamics simulation to run once again? If so, then will the
exact same molecules that adsorbed on the first MD run be the same
ones that adsorb on the second MD run?
The original coordinates are used to re-calculate the energies. No
new simulation is 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...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
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
simulation, which of these > molecules would adsorb.
Are you suggesting that, after the initial simulation run, which
uses an > index file "index.ndx" and is comprised of three
components {System, > Grph, NH3}, I run make_ndx again to assign
each adsorbed molecule to its > own index, execute "mdrun -rerun
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?
Almost. You can't use the original .tpr file if you are trying to
establish new energy monitoring groups. Hence the point of making a
new .mdp file. So, re-run the old trajectory with the new .tpr file
to take advantage of the new groups.
-Justi
Re: [gmx-users] Adsorption energy of a single molecule
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?
Not necessarily, unless the force field was parameterized to produce
such values. First, seek to define what you mean by adsorption (free)
energy, then consider how a simulation might measure that. Then,
consider whether any force fields exist that might achieve that. Then,
test it on a case where you have experimental data.
Other procedures run a much higher risk of producing an expensive random
number generator :-)
And will this energy be just
the interaction energy between the adsorbed molecule and the graphene
sheet (i.e. does the creation of the new index file and executing -rerun
cause g_energy to exclude the energies between the other molecules and
the graphene sheet)?
Creating an energy group causes mdrun -rerun to report the fraction of
the total nonbonded energies that are due to intra- and inter-group
interactions. See manual section 3.3
Mark
Date: Sun, 01 Nov 2009 21:27:19 -0500
From: "Justin A. Lemkul"
Subject: Re: [gmx-users] Adsorption energy of a single molecule
To: Discussion list for GROMACS users
Message-ID: <4aee4387.40...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Darrell Koskinen wrote:
Hi Justin,
Since I cannot use the original .tpr file, then do I need to run
grompp with the new index file to create a "new" .tpr file,
"mdtopolnew.tpr"? I assume I then need to modify the energygrps line
within the .mdp file to include these new energy groups and then
execute "mdrun -rerun mdtraj.trr -s mdtopolnew.tpr". Is this correct?
Yes, that is the point of the -rerun function.
Does executing "mdrun -rerun mdtraj.trr -s mdtopolnew.tpr" cause a
molecular dynamics simulation to run once again? If so, then will the
exact same molecules that adsorbed on the first MD run be the same
ones that adsorb on the second MD run?
The original coordinates are used to re-calculate the energies. No
new simulation is 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...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
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
simulation, which of these > molecules would adsorb.
Are you suggesting that, after the initial simulation run, which
uses an > index file "index.ndx" and is comprised of three
components {System, > Grph, NH3}, I run make_ndx again to assign
each adsorbed molecule to its > own index, execute "mdrun -rerun
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?
Almost. You can't use the original .tpr file if you are trying to
establish new energy monitoring groups. Hence the point of making a
new .mdp file. So, re-run the old trajectory with the new .tpr file
to take advantage of the new groups.
-Justin
-- Justin A. Lemkul Ph.D.
Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia
Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Adsorption energy of a single molecule
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 adsorbed molecule and the graphene sheet (i.e. does the creation of the new index file and executing -rerun cause g_energy to exclude the energies between the other molecules and the graphene sheet)? Unless you have set some special energygrp_excl in the .mdp file, then nothing should be excluded; the use of energygrps simply decomposes the energy terms into the species of interest. As for what the adsorption energy is, it may well be LJ(SR), provided there are no Coulombic terms to worry about, but I don't know anything about your parameters, so I can't say definitively. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Adsorption energy of a single molecule
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 adsorbed molecule and the graphene
sheet (i.e. does the creation of the new index file and executing -rerun
cause g_energy to exclude the energies between the other molecules and
the graphene sheet)?
Thanks.
Darrell
Date: Sun, 01 Nov 2009 21:27:19 -0500
From: "Justin A. Lemkul"
Subject: Re: [gmx-users] Adsorption energy of a single molecule
To: Discussion list for GROMACS users
Message-ID: <4aee4387.40...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Darrell Koskinen wrote:
Hi Justin,
Since I cannot use the original .tpr file, then do I need to run grompp
with the new index file to create a "new" .tpr file, "mdtopolnew.tpr"? I
assume I then need to modify the energygrps line within the .mdp file to
include these new energy groups and then execute "mdrun -rerun
mdtraj.trr -s mdtopolnew.tpr". Is this correct?
Yes, that is the point of the -rerun function.
Does executing "mdrun -rerun mdtraj.trr -s mdtopolnew.tpr" cause a
molecular dynamics simulation to run once again? If so, then will the
exact same molecules that adsorbed on the first MD run be the same ones
that adsorb on the second MD run?
The original coordinates are used to re-calculate the energies. No new
simulation is 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...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
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
simulation, which of these > molecules would adsorb.
Are you suggesting that, after the initial simulation run, which
uses an > index file "index.ndx" and is comprised of three components
{System, > Grph, NH3}, I run make_ndx again to assign each adsorbed
molecule to its > own index, execute "mdrun -rerun 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?
Almost. You can't use the original .tpr file if you are trying to
establish new energy monitoring groups. Hence the point of making a new
.mdp file. So, re-run the old trajectory with the new .tpr file to take
advantage of the new groups.
-Justin
-- Justin A. Lemkul Ph.D.
Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia
Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Adsorption energy of a single molecule
Darrell Koskinen wrote:
Hi Justin,
Since I cannot use the original .tpr file, then do I need to run grompp
with the new index file to create a "new" .tpr file, "mdtopolnew.tpr"? I
assume I then need to modify the energygrps line within the .mdp file to
include these new energy groups and then execute "mdrun -rerun
mdtraj.trr -s mdtopolnew.tpr". Is this correct?
Yes, that is the point of the -rerun function.
Does executing "mdrun -rerun mdtraj.trr -s mdtopolnew.tpr" cause a
molecular dynamics simulation to run once again? If so, then will the
exact same molecules that adsorbed on the first MD run be the same ones
that adsorb on the second MD run?
The original coordinates are used to re-calculate the energies. No new
simulation is 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...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
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
simulation, which of these > molecules would adsorb.
> > Are you suggesting that, after the initial simulation run, which
uses an > index file "index.ndx" and is comprised of three components
{System, > Grph, NH3}, I run make_ndx again to assign each adsorbed
molecule to its > own index, execute "mdrun -rerun 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?
>
Almost. You can't use the original .tpr file if you are trying to
establish new energy monitoring groups. Hence the point of making a new
.mdp file. So, re-run the old trajectory with the new .tpr file to take
advantage of the new groups.
-Justin
-- Justin A. Lemkul Ph.D.
Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia
Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
___
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
___
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Adsorption energy of a single molecule
Hi Justin,
Since I cannot use the original .tpr file, then do I need to run grompp with the new index file to create a
"new" .tpr file, "mdtopolnew.tpr"? I assume I then need to modify the energygrps line
within the .mdp file to include these new energy groups and then execute "mdrun -rerun mdtraj.trr -s
mdtopolnew.tpr". Is this correct?
Does executing "mdrun -rerun mdtraj.trr -s mdtopolnew.tpr" cause a molecular
dynamics simulation to run once again? If so, then will the exact same molecules that
adsorbed on the first MD run be the same ones that 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] Adsorption energy of a single molecule
To: Discussion list for GROMACS users
Message-ID: <4aee27f0.50...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
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 simulation, which of these
> molecules would adsorb.
>
> Are you suggesting that, after the initial simulation run, which uses an
> index file "index.ndx" and is comprised of three components {System,
> Grph, NH3}, I run make_ndx again to assign each adsorbed molecule to its
> own index, execute "mdrun -rerun 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?
>
Almost. You can't use the original .tpr file if you are trying to establish new
energy monitoring groups. Hence the point of making a new .mdp file. So,
re-run the old trajectory with the new .tpr file to take advantage of the new
groups.
-Justin
-- Justin A. Lemkul Ph.D.
Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia
Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
___
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Adsorption energy of a single molecule
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 simulation, which of these
molecules would adsorb.
Are you suggesting that, after the initial simulation run, which uses an
index file "index.ndx" and is comprised of three components {System,
Grph, NH3}, I run make_ndx again to assign each adsorbed molecule to its
own index, execute "mdrun -rerun 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?
I don't know what Justin suggested, but a re-run with each ammonia in
its own energy group ought 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: <4aed7c54.2080...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Darrell Koskinen wrote:
Hi Justin,
Thanks for the suggestion. I looked through the GROMACS manual and
the only method I can see of obtaining the adsorption energy between
an adsorbed ammonia molecule and the graphene sheet would be to
create an index file that assigns a separate index for each ammonia
molecule, run the simulation, and then run "gmxdump -e mdener.edr" to
view the energy between the adsorbed ammonia molecule and the
graphene sheet. Is this the method you are suggesting or is there a
different method of obtaining this information?
From your original message, I got the impression that only a few of
your ammonia molecules were adsorbed. In this case, a better approach
might be to identify the molecules that adsorbed in your original
simulation, create groups for those individually, the graphene sheet,
and then the rest of your ammonia. Then 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: Discussion list for GROMACS users
Message-ID: <4ae9d9a3.9080...@vt.edu>
Content-Type: text/plain; charset=UTF-8; format=flowed
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 the adsorption energy of a single
molecule to that reported in research papers.
You should be able to study interactions between individual
molecules by using energygrps and an appropriate index file.
-Justin
Thanks.
Darrell
___
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
___
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Adsorption energy of a single molecule
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 simulation, which of these
molecules would adsorb.
Are you suggesting that, after the initial simulation run, which uses an
index file "index.ndx" and is comprised of three components {System,
Grph, NH3}, I run make_ndx again to assign each adsorbed molecule to its
own index, execute "mdrun -rerun 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?
Almost. You can't use the original .tpr file if you are trying to establish new
energy monitoring groups. Hence the point of making a new .mdp file. So,
re-run the old trajectory with the new .tpr file to take advantage of the new
groups.
-Justin
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
___
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Adsorption energy of a single molecule
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 simulation, which of these
molecules would adsorb.
Are you suggesting that, after the initial simulation run, which uses an
index file "index.ndx" and is comprised of three components {System,
Grph, NH3}, I run make_ndx again to assign each adsorbed molecule to its
own index, execute "mdrun -rerun 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 energy of a single molecule
To: Discussion list for GROMACS users
Message-ID: <4aed7c54.2080...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Darrell Koskinen wrote:
Hi Justin,
Thanks for the suggestion. I looked through the GROMACS manual and the
only method I can see of obtaining the adsorption energy between an
adsorbed ammonia molecule and the graphene sheet would be to create an
index file that assigns a separate index for each ammonia molecule, run
the simulation, and then run "gmxdump -e mdener.edr" to view the energy
between the adsorbed ammonia molecule and the graphene sheet. Is this
the method you are suggesting or is there a different method of
obtaining this information?
From your original message, I got the impression that only a few of your
ammonia molecules were adsorbed. In this case, a better approach might be to
identify the molecules that adsorbed in your original simulation, create groups
for those individually, the graphene sheet, and then the rest of your ammonia.
Then 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: Discussion list for GROMACS users
Message-ID: <4ae9d9a3.9080...@vt.edu>
Content-Type: text/plain; charset=UTF-8; format=flowed
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 the adsorption energy of a single
molecule to that reported in research papers.
You should be able to study interactions between individual molecules
by using energygrps and an appropriate index file.
-Justin
Thanks.
Darrell
___
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Adsorption energy of a single molecule
Darrell Koskinen wrote: Hi Justin, Thanks for the suggestion. I looked through the GROMACS manual and the only method I can see of obtaining the adsorption energy between an adsorbed ammonia molecule and the graphene sheet would be to create an index file that assigns a separate index for each ammonia molecule, run the simulation, and then run "gmxdump -e mdener.edr" to view the energy between the adsorbed ammonia molecule and the graphene sheet. Is this the method you are suggesting or is there a different method of obtaining this information? From your original message, I got the impression that only a few of your ammonia molecules were adsorbed. In this case, a better approach might be to identify the molecules that adsorbed in your original simulation, create groups for those individually, the graphene sheet, and then the rest of your ammonia. Then 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: Discussion list for GROMACS users Message-ID: <4ae9d9a3.9080...@vt.edu> Content-Type: text/plain; charset=UTF-8; format=flowed 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 the adsorption energy of a single molecule to that reported in research papers. You should be able to study interactions between individual molecules by using energygrps and an appropriate index file. -Justin Thanks. Darrell ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Adsorption energy of a single molecule
Hi Justin, Thanks for the suggestion. I looked through the GROMACS manual and the only method I can see of obtaining the adsorption energy between an adsorbed ammonia molecule and the graphene sheet would be to create an index file that assigns a separate index for each ammonia molecule, run the simulation, and then run "gmxdump -e mdener.edr" to view the energy between the adsorbed ammonia molecule and the graphene sheet. Is this the method you are suggesting or is there a different method of obtaining this information? 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: Discussion list for GROMACS users Message-ID: <4ae9d9a3.9080...@vt.edu> Content-Type: text/plain; charset=UTF-8; format=flowed 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 the adsorption energy of a single molecule to that reported in research papers. You should be able to study interactions between individual molecules by using energygrps and an appropriate index file. -Justin Thanks. Darrell ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Adsorption energy of a single molecule
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 the adsorption energy of a single molecule to that reported in research papers. You should be able to study interactions between individual molecules by using energygrps and an appropriate index file. -Justin Thanks. Darrell ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Adsorption energy of a single molecule
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 single molecule to that reported in research papers. Thanks. Darrell ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
