Hello everyone,
i am currently working on the effects of temperature on a system but with my current mdp setting the results are not looking realistic. Curently 300K and 600K are giving the similar values which shouldnt be so. i will like to know how to set up my mdp file in a way that the temperature is increased from one side of system before circulating through the whole system. Or any special settings to include for a temperature dependent simulation.
Thanks.
Dear Bukunmi,
You can try to couple different groups of your system to different temperature baths. If you freeze positions of certain atoms in molecules on one side, you will get the 600K bath on one side of the system whereas the rest of the system is coupled to 300K. However, the heat diffuse to the mirror image of the system and heat up the other side as well. Thus you should carefully choose which atoms to freeze/heat up. The result depends on the topology of the system though. If you provide more details of your system and describe what you are looking for, you might get a better help.
Up to date I am not aware of an anisotropic temperature coupling implementation in Gromacs.
Best regards,
Alexandr
Here you can find options for temperature change:
I left comments in brackets.
; SIMULATED ANNEALING
; Type of annealing for each temperature group (no/single/periodic)
annealing = (you can choose one of these options f.ex. single)
; Number of time points to use for specifying annealing in each group
annealing-npoints = 6 (how many times would you like to increase temperature?)
; List of times at the annealing points for each group
annealing-time = 0 2000 4000 10000 15000 20000 (simulation time when temperature changes)
; Temp. at each annealing point, for each group.
annealing-temp = 300 330 380 400 450 600 (temperature that system maintain according to simulation time)
Hi,
Was the question about how to have temperature distribution inside the simulation box? If so, neither simulated annealing nor replica exchange solve the problem since they produce ensembles at constant temperatures.
-Alexandr
Thanks everyone, though i mentioned that 300K and 600K give the same results because thats the temperature range but i am actually working with 300K with 50K increase till 600K so 350K, 400K, 450K...gave me similar results which i believe shouldnt be so since water gains more momentum with temperature and that should affect my results as well. Alexandr your answer would have been perfect if i was only interested in one temperature but i have a range, Jamoliddin yes i used simulated annealing but should i keep the temperature of my sample constant throughout the simulation time( as suggested by Alexandr) while i increase that of water environment? Pritam, REMD is totally new to me but i will run a test.
Thanks
Bukunmi
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