search

fhh2626 / BFEE2

binding free energy estimator 2
GNU General Public License v3.0
101 stars 32 forks source link

Mistakes with the tempetarute targets #121

Open groponp opened 5 months ago

groponp commented 5 months ago

Dear all,

I'm experience the following mistakes:

1) I have prepared my system using charmm-gui (protein-ligand). when I run the equilibration step the target temperature is in average 309 K (my target is 310.15) which do sense. But when I run the production the average temperature is about 307 K, Which is the motive to it? . Note: Langevin thermostats is used.

2) When I change from langevin to veolicity rescaling (busi) thermostat my simulation keep about 310 K, but I want to know if is right to using the second one thermostat.

fhh2626 commented 3 months ago
  1. I am not sure, but the error seems OK.
  2. You can always turn to the Bussi thermostat if you want.
groponp commented 3 months ago

Do exists any limitation with bussi thermostat?

fhh2626 commented 2 months ago

I don't think there is an obvious limitation with the bussi thermostat

groponp commented 2 months ago

Is it right to use with FEP or TI? , because I have read that bussi thermostat can have problems with it.

Thanks so much for your help in advanced.