[gmx-users] using one thermostat for entire system ??

[Jennifer Williams]

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 <Mark.Abraham at anu.edu.au>:

> 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
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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


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