Thanks Mark for the advice.
I have just rerun a test simulation with each of my gas species
coupled separately to a thermostat and have got similar values for the
quantities of interest (diffusion coefficients). However I am not sure
that this will satisfy the reviewer without a bit more justification
of why I chose to use a single thermostat for my system.
I remembered reading some gromacs information on the application of
thermostats (on which I based my decision to apply one thermostat for
the entire system). I have just managed to locate it on the FAQ page:
http://www.gromacs.org/Documentation/Terminology/Thermostats
What Not To Do
Some hints on practices that generally not a good idea to use:
? Do not use separate thermostats for every component of your system.
Some molecular dynamics thermostats only work well in the
thermodynamic limit. A group must be of sufficient size to justify
its own thermostat. If you use one thermostat for, say, a small
molecule, another for protein, and another for water, you are likely
introducing errors and artifacts that are hard to predict. In
particular, do not couple ions in aqueous solvent in a separate group
from that solvent.
My system consists of
55 molecules of CO2
38 molecules of N2
3 molecules of O2
One large molecule of MCM-41 (mostly frozen but with mobile surface
groups) consisting of 4284 atoms.
My take on this was that the gas molecules were in small supply
compared to the other part of the system so I should avoid using
separate thermostats. Was I mistaken in making this assumption?
Is there any feeling for what "sufficient size" as referred to above
is? Does anyone know of any papers I could reference in my explanation?
Any comments welcome
Thanks
Jenny
Quoting Mark Abraham <[email protected]>:
On 8/03/2011 2:50 AM, Jennifer Williams wrote:
Hi,
I simulated the diffusion of small gases (CO2, N2) in a framework
structure which was mostly frozen with some mobile surface groups.
I applied a temperature thermostat to the entire system (i.e I
didn't couple the gas molecules and framework separately). I have
now been asked the following by a reviewer:
"Please comment on any artefacts that might arise as a result of
non-equipartition of energies. For example, what is the calculated
temperature of each of the gas species and mobile species?"
I have tried to explore the temperature of each species separately
but g_energy will only give me the energy of the system as a whole.
Are there any other tools within gromacs to look at the temperature
of each species in turn from the md runs I already have?
Does anyone have a suggestion as to how I can address the
reviewer's comment and proove that using one thermostat for the
whole system is OK (that is what I am hoping!). Is there anything
in particular that I should be looking closely at?
g_energy can only report the global temperature as saved in the .edr
file, computed during the simulation. The only way of decomposing
the temperature is to save velocities to the .trr file with nstvout.
(Some colleagues had to do this recently.) Then, judicious use of
trjconv to take subsets and matching topology hacking (tpbconv
doesn't quite work) mean you can use mdrun -rerun on the subset .trr
and matching .tpr to get a group-wise temperature. That can
demonstrate whether temperature differentials (ie. heat flows) exist.
If you didn't save velocities, you're out of luck.
Mark
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Dr. Jennifer Williams
Institute for Materials and Processes
School of Engineering
University of Edinburgh
Sanderson Building
The King's Buildings
Mayfield Road
Edinburgh, EH9 3JL, United Kingdom
Phone: ++44 (0)131 650 4 861
--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
