[gmx-users] thermostat

[Hosein Geraili Daronkola]

Hi,

I want to study the dynamics of protein and waters around it for a long
simulation, but when using Langevin thermostat (SD integrator), it will
decrease the diffusion and other dynamical properties of my system. Is
using no tcoupl on protein and using 10 ps on just solvent (noninvasive
method) non_physical?? If yes how can I not use scaling thermostats (
Nose-Hoover, or Berendesen becuase they are not ergodic), and have the
almost same dynamics as the NVE ensemble for 1 microsecond long simulation
of a protein in water?? Maybe using 100 ps relaxation time on protein and
10 ps on solvent?

Best

-- 
Hosein Geraili Daronkola
Ph.D. student,

Wissenschaftspark Potsdam-Golm
Max Planck Institute of Colloids and Interfaces
Theory and Bio-Systems Department

Office K-1.119
Am Mühlenberg 1 OT Golm
14476 Potsdam
Germany

Phone: +49-(0)331 567-9611
Fax: +49-(0)331 567-9602
E-mail: hosein.geraili at mpikg.mpg.de


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11/28/18,
6:03:24 PM