In some articles authors have carried out MD in Gromacs by slowly increasing the temperature. I wanted to perform such a technique for my work by increasing the temperature slowly from 300 to 310 K during MD. I have no idea how to edit the md.mdp file to seek such techniques. Hoping for a positive response.
Thank you.
Simulated annealing is one of the possible way to do this...
http://manual.gromacs.org/online/mdp_opt.html#sa
You should use REMD http://www.gromacs.org/Documentation/How-tos/REMD
They probably just ran successive simulations and changed the temperature in each simulation... say from 300K to 310K at 1 degree increment using 11 simulations.
I think REMD is not what you are looking for...
Dear Balder Lai,
I think it is not a wise way to perform by generating multiple .tpr files with periodic Md simulation. I wanted to analyze my system in a continuous way.
Simulated annealing is one of the possible way to do this...
http://manual.gromacs.org/online/mdp_opt.html#sa
You have to perform multi step MD with different md.mdp files
Norbert
With a single simulation this can be easily performed; simulated annealing. In the heating.mdp file use two temperatures, 0 to 300 K and two annelating points may be 0 to 300 ps
Then use proper coupling constant with a good thermostat (Berendsen) and u r done.
http://manual.gromacs.org/online/mdp_opt.html#sa
http://lists.gromacs.org/pipermail/gmx-users/2012-June/072342.html
I think you must use to tاermostat for example Nose-Hoover thermostatو...
You can specify your desired temperature with "ref_t = 310" in the md.mdp file and use this with grompp in each continuation run (unlike tpbconv to extend the runs). And keep the velocity_generation off in it.
You do not need to prepare separate .mdp files and run different simulations with them. You can use any of the thermostats available in GROMACS with simulated annealing:
http://manual.gromacs.org/online/mdp_opt.html#sa
Just write the timesteps at which to increase the temperature and the same number of temperature values in the .mdp file (grompp will throw and error and tell you to fix this otherweise). You can also define different groups for temperature coupling and supply different values for each.
In a single simulation you can go for SA but, your objective should be very much clear. you can modified the attachment according to you need.
Good Luck
http://gromacs.5086.x6.nabble.com/Simulated-Annealing-Protocol-td4625020.html
you edit md.mp through notepad (in case of windows) and gedit /vi editor (in case of linux) program.
1st change Generate velocites >>>>>> provide temprature (your choice)
2nd change ref_t for protein and non-protein.
Hi everyone
I am using the attach mdp file for increasing the temp from 0 to 300k. Can anyone help me to fix the problem.
I have used this and it tell me the fatal error:
Not enough annealing values: 1 (for 2 groups)
Fetal error : Only bcoz you have not given the time steps for running temp.
If you are simulating Protein in water than better keep " tc-grps = system" and similarly tau_t = 0.1 0.1 ;
ref_t = 300 300 to tau_t = 0.1 & ref_t=300
; SIMULATED ANNEALING CONTROL
annealing = single
annealing-npoints = 2
annealing-time = 0 2000
annealing-temp = 0 300
If you are running protein- RNA/DNA/metal ions/ligands than you have to use what you have given and do little change in annealing protocol i.e.,
annealing = single single
annealing-npoints = 2 2
annealing-time = 0 2000 0 2000
annealing-temp = 0 300 0 300
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