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 thermostat as described in (T. Soddemann

[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

RE: [gmx-users] stochastic dynamics , langevin

kinetic quantity that you are interested in. For different quantities tau_t can be different. Berk Date: Thu, 23 Oct 2008 15:31:16 +0200 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: [gmx-users] stochastic dynamics , langevin Dear All, I am trying to perform Langevin dynamics of large

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 pick

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

tau_t to reproduce some kinetic quantity that you are interested in. For different quantities tau_t can be different. Berk Date: Thu, 23 Oct 2008 15:31:16 +0200 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: [gmx-users] stochastic dynamics , langevin Dear All, I am trying to perform