[gmx-users] stochastic dynamics , langevin
gmx3 at hotmail.com
Fri Oct 24 12:29:36 CEST 2008
> From: mihoopes at ucdavis.edu
> To: gmx-users at 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
> 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, 68:046702,
> (b) if nothing approaches DPD, how would a one go about starting to write a
> new thermostat in GROMACS?
Implementing a new thermostat in Gromacs is easy, except for DPD,
since it interferes both with the neighborlist and the integration.
I have considered implementing DPD, but it is a lot of work
and also difficult to do efficiently, since the DPD interactions are
more expensive that the Coulomb and LJ interactions.
Note that you only really need DPD for non-equilibrium phenomena
where hydrodynamics plays a role.
> Matthew Hoopes
> Biophysics Graduate Group
> University of California, Davis
> mihoopes at ucdavis.edu
> Brownina dynamics is a Langevin equation for the coordinates (no inertia).
> Stochastic dynamics is a Langevin equation for the velocities (with
> 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 sampling is nonsense.
> tau_t has no effect on the distribution, only on the dynamics. If you want
> the correct dynamics, you will have fit tau_t to reproduce some kinetic
> quantity that you are interested in. For different quantities tau_t can be
> Date: Thu, 23 Oct 2008 15:31:16 +0200
> From: omermar at gmail.com
> To: gmx-users at gromacs.org
> Subject: [gmx-users] stochastic dynamics , langevin
> Dear All,
> I am trying to perform Langevin dynamics of large peptides / proteins. After
> reading the manual & going over some old mails in this list, I have two
> points I hope you could clear for me:
> [Gromacs version 3.3.3]
> 1) I am a bit confused with Brownian vs. Langevin dynamics. Is this the
> proper keywords I should use for Langevin dynamics: integrator = sd ;
> bd-fric = 0 ;
> tau_t = 10 ;
> ref_t = 300 ;
> With bd-fric=0, the friction is taken as the inverse tau_t.
> 2) From your experience, what are good values of tau_t (or 1/tau_t) for
> simulating a protein? In 2006 list, David has commented that choosing tau_t
> is very important (
> http://www.gromacs.org/pipermail/gmx-users/2006-July/023089.html ).
> Your help is appreciated. Omer.
> Koby Levy research group,
> Weizmann Institute of Science.
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