[gmx-users] How does g_msd calculates MSD?

as the second half (with the proper shifting) of the output of g_msd -b 0 -e 100 -trestart 50 But it is not, as anyone can verify with any simulation. .. what are we missing? Thanks in advance, Julian -- Julian Gelman Constantin Department of Inorganic, Analytic and Chemical Physics (DQIAQF

[gmx-users] Langevin thermostat implementation in GROMACS vs AMBER

) Is 'bd-fric' of GROMACS equivalent to 'gamm_ln' of AMBER ? Thanks for your help, Julian -- Julian Garrec, research associate Web: https://sites.google.com/site/juliangarrec/ Équipe : Chimie et Biochimie Théoriques Unité Mixte de Recherches CNRS UHP 7565 Université de Lorraine, Nancy I BP 239

Re: [gmx-users] Langevin thermostat implementation in GROMACS vs AMBER

such as the friction coeficient in equation 3.114 of the manual (v4.6.1). Please help, Sincerely, Julian Le 04/05/13 13:42, Julian Garrec a écrit : Dear all, I am trying to use stochastic dynamics in GROMACS to reproduce some previous results that I got with the AMBER software using

Re: [gmx-users] Re: Langevin thermostat implementation in GROMACS vs AMBER

Le 08/05/13 19:33, Christoph Junghans a écrit : Date: Wed, 08 May 2013 16:34:46 +0200 From: Julian Garrec julian.gar...@epfl.ch Subject: Re: [gmx-users] Langevin thermostat implementation in GROMACS vs AMBER To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID

[gmx-users] problem with position restraints: X0 set to zero

+00), fcB=( 5.6700e+02, 5.6700e+02, 5.6700e+02) Using the -debug option with grompp didn't provide me further information. Does anybody know how to cure this problem ? Thanks, Julian -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx

Re: [gmx-users] problem with position restraints: X0 set to zero

Justin A. Lemkul wrote: Julian Garrec wrote: Justin A. Lemkul wrote: Julian Garrec wrote: Dear GROMACS users, I am trying to equilibrate my system (monomeric protein in water) and I want to use position restraint on heavy atoms of the solute using the posre.itp file

[gmx-users] electrostatic component of the forces

and vdw components from the forces ? One option could be to set all the unwanted interaction to zero in the topology file but I am wondering if there is a safer alternative. Cheers, -- Julian Garrec, post-doc Tel: ++41 (0)21 69 303 27 Web: https://sites.google.com/site/juliangarrec

Re: [gmx-users] electrostatic component of the forces

Thank you very much for your clear reply. Best regards, Julian Garrec Le 25/05/12 17:17, Mark Abraham a écrit : On 25/05/2012 7:44 PM, Julian Mondon-Garrec wrote: Hi all, I am trying to get the electrostatic forces acting on each atom as a function of time. I have checked the list and all