RE: [gmx-users] stochastic dynamics , langevin

> From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Subject: RE: [gmx-users] stochastic dynamics , langevin > Date: Thu, 23 Oct 2008 15:32:02 -0700 > > Along these same lines... > (a)is there an thermostat setting in GROMACS that comes close to the DPD > therm

RE: [gmx-users] stochastic dynamics , langevin

Along these same lines... (a)is there an thermostat setting in GROMACS that comes close to the DPD thermostat as described in (T. Soddemann, B. D¨unweg, and K. Kremer. Dissipative particle dynamics: A useful thermostat for equilibrium and nonequilibrium molecular dynamics simulations. Phys. Rev. E,

Re: [gmx-users] stochastic dynamics , langevin

Berk Hess wrote: > Everything depends on what you want to do, which you do not tell in detail. > If you want to leave out the solvent, but you want to simulate a system > in solvent, > SD is not going to help you, since there is no implicit solvent potential, > so your potential and therefore your

Re: [gmx-users] stochastic dynamics , langevin

Thanks for the quick reply Berk. > > 1) Is this the proper keywords I should use for Langevin dynamics: > integrator = sd ; > bd-fric= 0 ; > tau_t = 10 ; > ref_t = 300 ; > Basically, I want to know if I am using the 4 parameters correctly. That is - for Langevin dynamics, I should

RE: [gmx-users] stochastic dynamics , langevin

Hi, Brownina dynamics is a Langevin equation for the coordinates (no inertia). Stochastic dynamics is a Langevin equation for the velocities (with inertia). Everything depends on what you want to do, which you do not tell in detail. If you want to leave out the solvent, but you want to simulate a