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
Tot-Drift
-------------------------------------------------------------------------------
Total-Energy -464122 10572.6 0 -58.7363
-36651.5
The drift seems to me quite large compare to other simulations.
Shouldn't the energy be constant in NVE?
thanks for helping,
loris....
Berk Hess wrote:
From: lorix <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <[email protected]>
To: Discussion list for GROMACS users <[email protected]>
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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