[gmx-users] on NVE and pressure
gmx3 at hotmail.com
Mon Apr 16 14:18:35 CEST 2007
>From: lorix <Loris.Moretti at pharm.unige.ch>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Subject: Re: [gmx-users] on NVE and pressure
>Date: Mon, 16 Apr 2007 12:25:15 +0200
>Hi Berk and Jelger,
>Thanks for your comments...
>Yes I equilibrated the system with Berendsen thermostat and barostat for
>100ps and 200 ps and then switched them off.
>I thought that the coupling could have an influence in the final
>trajectory, because of the atom velocities scaling (?).
>Why does not make sense to run NVE after NPT?
You don't specify what your goals are, so I have to guess what you want.
MD is inherently chaotic and velocity correlations decay quickly,
so using NVE does, in general, not provide "better" velocities than NVT.
NVT is usually what you want when your system is in thermal equilibrium.
Only when you have energy dissipation after an event which takes your system
out of thermal equilibrium, i.e. pumps energy into the system,
it makes sense to use NVE.
However, when you equilibrate using NVT, this energy will already be
>The two systems (15000 and 40000 atoms) I am simulating at NVE both show
>increasing total energy:
>The first system had -154442 kJ mol^-1 as average for the 7-207 psec NPT
>equilibration and -168837 kJ mol^-1 as average value for 1500-2000 ps of
>The second system had -445679 kJ mol^-1 as average for the 14-114 psec NPT
>equilibration and -465630 kJ mol^-1 as average for the 300-600 ps of NVE
For energy conservation you should not look at the average energy,
but the energy drift during your NVE simulation.
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