Using the thermostat into NAMD

Question

Using the thermostat into NAMD

Opened this issue 9 months ago · 4 comments

Dear Giovanni,

I'm running a system protein-protein interaction on water, I want use the bussi thermostat into namd, but don't sure if is suitable on NAMD. I want perform equilibration with langevin thermostat but perform production with your thermostat, Is suitable it?

Answer 1 · 2024-03-13T15:17:19.000Z

Sorry I don't understand the question. Are you asking if it's implemented in NAMD? This I do not know. Are you asking if it's ok to equilibrate with Langevin and then use stochastic velocity rescaling? Yes it is

Answer 2 · 2024-03-13T15:20:09.000Z

Is last question. The thermostat is adequate to use into ABF, FEP methods? or Is only useful into classical md?.

Answer 3 · 2024-03-13T15:23:23.000Z

In principle it is. In practice, if you use FEP with annihilation, it might lead to issues at one boundary. So you have to test

Answer 4 · 2024-03-13T16:03:11.000Z

Thank so much for your help.