Re: [gmx-users] Large fluctuation of protein temperature with nose hoover thermostat

2009-09-17 Thread ABEL Stephane 175950
OK thank you Omer, for you response The group PROTEIN isn't very large as the group NONPROTEIN, therefore its total kinetic energy fluctuates more. --Omer. On Wed, Sep 16, 2009 at 12:10, Stephane Abel wrote: > tc-grps = Protein Non-Protein ; two coupling groups - more accurate > tau_t = 0.4 0

Re: [gmx-users] Large fluctuation of protein temperature with nose hoover thermostat

2009-09-17 Thread Omer Markovitch
The group PROTEIN isn't very large as the group NONPROTEIN, therefore its total kinetic energy fluctuates more. --Omer. On Wed, Sep 16, 2009 at 12:10, Stephane Abel wrote: > tc-grps = Protein Non-Protein ; two coupling groups - more accurate > tau_t = 0.4 0.4 ; time constant, in ps > ref_t = 310

[gmx-users] Large fluctuation of protein temperature with nose hoover thermostat

2009-09-16 Thread Stephane Abel
Hi gromacs experts, For my simulations of peptide (8 AA) in water (5100, SPC/E) and with 1 Cl- i use the Nose-Hoover Thermostat to simulate in NVT ensemble. Since i am a beginner with GROMACS, i have a question with the tau_t parameters Parameters i used I ; Temperature coupling is on tcoupl