sure, what room number in Palmer?
Andrew Stelzer
The University of Michigan
Chemical Biology Doctoral Program
Department of Chemistry &
Biophysics Research Division
900 N. University
Ann Arbor, MI 48109
On Apr 16, 2007, at 9:33 AM, lorix wrote:
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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