[gmx-users] on NVE and pressure

lorix Loris.Moretti at pharm.unige.ch
Mon Apr 16 15:33:04 CEST 2007

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.

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,

Berk Hess wrote:

>> 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 
> dissipated.
>> 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 NVE.
>> 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 equilibration.
> For energy conservation you should not look at the average energy,
> but the energy drift during your NVE simulation.
> Berk.
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