[gmx-users] Re: Tcoupl default setting

Thank you Mark for your response, In carrying out the test you recommended I realised that I had set the integrator to sd, in such a case the tcoupl parameter is ignored. This explains my well behave temperature in the absence of setting a tcoupl option. When I wrote the input file

[gmx-users] Tcoupl default setting

Dear All, I had intended to perform an NPT simulation, however although I selected a barostat I omitted to select a thermostat, nevertheless I did set tc_grps= system, tau_t = 0.1 and ref_t= 300. My temperature appears to fluctuate around the desired 300 K. My question is, by setting tau_t

[gmx-users] Tcoupl default setting‏

Dear All, I had intended to perform an NPT simulation, however although I selected a barostat I omitted to select a thermostat, nevertheless I did set tc_grps= system, tau_t = 0.1 and ref_t= 300. My temperature appears to fluctuate around the desired 300 K. My question is, by setting tau_t

[gmx-users] Amb2gmx

Dear all, Lennard Jones radius parameters are converted between gromacs and amber with the conversion factor (2**(5/6))/10 in the amb2gmx script. While I understand that the 10 takes care of the Angstrom to nanometers conversion I do not understand the origin of the 2 to the power of 5/6. I