Re: [gmx-users] direction_periodic

You did suggest that, but it crashes at step 0, as said :) Alex Berk Hess schrieb: > Hi, > > Then you should use constraint pulling instead of an umbrella potential. > I have been wondering all the time why you are using a potential > and not a constraint. I think I had suggested using a constrai

Re: [gmx-users] direction_periodic

Hey, I want to pull the diamonds with more or less exactly the speed I give for the pulling without the massive noise (in gromacs 3.3 this worked using afm type pulling, after some equilibration the slabs settled to an almost constant pull speed without soo much fluctuation using the same paramete

Re: [gmx-users] non isotropic kinetic energy

Berk Hess schrieb: > Equipartitioning only works per degree of freedom, not per atom. > > It works for translation and rotation of a water molecule, > but that requires a transformation from atomic to COM trans and rot > coordinates. Agreed. As said, we have performed this transfomation using anot

Re: [gmx-users] non isotropic kinetic energy

Berk Hess schrieb: > Yes, we can agree that they are rigid bodies. > > I would say that you should get equipartitioning of rotational > degrees of freedom. > g_traj can compute rotational kinetic energies. > For you whole system you would have to make each water > an index group, select each water

Re: [gmx-users] non isotropic kinetic energy

> It is well known that water at a surface is ordered. How do you choose > the waters to analyze? If there is a net ordering in the system due to > external factors your system is not in equilibrium, but rather in a > steady state. However if you have e.g. vacuum-water-vacuum the > symmetry makes

Re: [gmx-users] non isotropic kinetic energy

Hi > > Have you tested the equipartitioning per atom? This must be correct. We have done per atom (here of course only ekin is available). Here the average ekin parallel to the interface deviates from the ekin perpendicular to the interface (this is the data in the zip file of the old mail). You c

Re: [gmx-users] non isotropic kinetic energy

Hi, I have done exactly what you suggest in your first paragraph, seperating translation and rotation for each water molecule. If you want I can send you the new ekin_vs_t_and_erot_vs_t.dat where you can see that the ekin is actually equidistributed but the erot isn't! So in this rigid body persp