Re: [gmx-users] Different temperatures for different groups, even with Nose-Hoover

The comment from Justin and your answer to it were pretty convincing. I think the problem is solved :)). Tom is correct to get T with g_energy on a simulation that ran with one Tcoup, you need to rerun the trajectory (trr) with a tpr in which you define two Tcoup. This should give you T for

[gmx-users] Different temperatures for different groups, even with Nose-Hoover

Hi, I'm using GROMACS 4.0.5 to do a MARTINI simulation of a CG protein in a CG water box, looking at the diffusion constant of the protein among other things. I'm using the Nose-Hoover thermostat and Parrinello-Rahman barostat with tc-grps = System. In CHARMM, a protein-in-water simulation with

Re: [gmx-users] Different temperatures for different groups, even with Nose-Hoover

On Oct 29, 2009, at 9:26 PM, Michael Lerner wrote: Hi, I'm using GROMACS 4.0.5 to do a MARTINI simulation of a CG protein in a CG water box, looking at the diffusion constant of the protein among other things. I'm using the Nose-Hoover thermostat and Parrinello-Rahman barostat with

Re: [gmx-users] Different temperatures for different groups, even with Nose-Hoover

Michael Lerner wrote: Hi, I'm using GROMACS 4.0.5 to do a MARTINI simulation of a CG protein in a CG water box, looking at the diffusion constant of the protein among other things. I'm using the Nose-Hoover thermostat and Parrinello-Rahman barostat with tc-grps = System. In CHARMM, a

Re: [gmx-users] Different temperatures for different groups, even with Nose-Hoover

On Thu, Oct 29, 2009 at 5:38 PM, Justin A. Lemkul jalem...@vt.edu wrote: I see you are using constraints = none, but are there any constraints defined in the topology? If so, as noted in g_traj -h: Option -ot plots the temperature of each group, provided velocities are present in the

Re: [gmx-users] Different temperatures for different groups, even with Nose-Hoover

On Thu, Oct 29, 2009 at 5:31 PM, XAvier Periole x.peri...@rug.nl wrote: On Oct 29, 2009, at 9:26 PM, Michael Lerner wrote: I calculated temperatures with g_traj -f md2.trr -s md2.tpr -n index.ndx -ot -ng 5 I did not know you could get the temperature throught g_traj ... the -ot option

Re: [gmx-users] Different temperatures for different groups, even with Nose-Hoover

To get g_energy to give you the temperature (or any other property) of a specific group you need to have defined appropriate energygrps in your mdp file. This is independent of the choice of groups you use for the temperature coupling. If you want to calculate these temperatures of the groups