[gmx-users] on NVE and pressure

Berk Hess gmx3 at hotmail.com
Tue Apr 17 11:30:00 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 15:33:04 +0200
>The goal of mine is to see whether I can simulate a large conformational 
>change on an protein.
>A relative movement of one part respect another one, a rearrangment of on 
>enzyme inactive state to its active one.
>When I started more than I year ago I thought this was the MD framework.
>I am modifing the inactive state, present in a crystallographic structure, 
>in a way that would lead to the conformational change and then simulating 
>as accurate as possible.
>I guess that what I am interesting in is the conformation evolution of the 
>protein system rather than monitoring parameters. For what I can understand 
>this evolution is deterministically correlated with the atom velocities. So 
>far I appreciated how trajectories changed depending on the initial 
>conditions and on the used settings and parameters.

MD is deterministic, but also chaotic.
A minimal change in initial conditions rapidly lead to uncorrelated
velocities. Therefore in more cases the "accuracy" of the velocities
is irrelevant.
Only when energy needs to be dissipated NVE in required instead of NVT.
But that does not seem to be what you are looking for.

>Statistics over 624001 steps [ 114.0000 thru 738.0000 ps ], 1 data sets
>Energy                      Average       RMSD     Fluct.      Drift  
>Total-Energy                -464122    10572.6          0   -58.7363   
>The drift seems to me quite large compare to other simulations.
>Shouldn't the energy be constant in NVE?
>thanks for helping,

59 on 464122 is quite small.
You should check how much it is in kT per degree of freedom,
probably very little.


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