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
