[gmx-users] heating

kiana moghaddam ki_moghaddam at yahoo.com
Tue Dec 3 08:20:25 CET 2013

Dear GMX Users

I want to run NVT equilibration and NPT equilibration (after NVT) and want to increase temperature gradually i.e. from 0 to 300 K over 100 ps, but I have some questions about this process:
when I use simulated annealing in NVT as following
annealing_time          =  0  15  30  45   60  80  100
annealing_temp          = 0  50 100 150 200 250 300
I don't know how to change gen_temp. Should gen_temp be 0 or 300 K?

At the first time, I did not use simulated annealing. I prepared 7 mdp files that in the first mdp file, I set nsteps=0, gen_temp=0, ref_t=0, then I use the output from first NVT equilibration for the second input. I repeat this to reach 300 K (in the second step nsteps=7500(*0.002=15), gen_temp=50, ref_t=50). I 'm not sure whether this process is correct?
Could you please help me? Thanks for your time and consideration.

Best Regards

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