problem.
Berk
> Date: Thu, 12 Mar 2009 10:55:47 +0100
> From: degaet...@dcci.unipi.it
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Re: Energy Drift in Gromacs 4.0
>
> Even if a system is not well equilibrated (but not so far from
> equilibrium) ,energy should be cons
even without switching of VdW
potential.
Luca Dre Gaetani
Message: 1
Date: Thu, 12 Mar 2009 13:59:11 +1100
From: Mark Abraham
Subject: Re: [gmx-users] Re: Energy Drift in Gromacs 4.0
To: Discussion list for GROMACS users
Message-ID: <49b87a7f.30...@anu.edu.au>
Content-Type: text
Ilya Chorny wrote:
Ok, I got it. Set electrostatics to PME-switch. Made rcoulomb-switch .1
less than rcoulomb and set rlist accordingly and now I am conserving
energy. Yipee!!!
It did not make sense to me that the system had to be fully relaxed to
conserve energy. It should conserve energy en
Ilya Chorny wrote:
If I plot the K.E(t) and P.E.(t) they are both going down. In an NVE
simulation they should counter balance. I am leaking K.E. somewhere. I
reran with a relaxed P.E(t) and saw the same behavior. This is
happening both at 2 and 4 fs so its not a time step issue. Any thoughts?
Ok, I got it. Set electrostatics to PME-switch. Made rcoulomb-switch .1 less
than rcoulomb and set rlist accordingly and now I am conserving energy.
Yipee!!!
It did not make sense to me that the system had to be fully relaxed to
conserve energy. It should conserve energy energy as long as it has be
If I plot the K.E(t) and P.E.(t) they are both going down. In an NVE
simulation they should counter balance. I am leaking K.E. somewhere. I reran
with a relaxed P.E(t) and saw the same behavior. This is happening both at
2 and 4 fs so its not a time step issue. Any thoughts? I thought it might
be
Ilya Chorny wrote:
Forgot column labels on energies.
Average
RMSD Fluct. Drift Tot-Drift
2 fs time step Total Energy46497.236445.6 2630.7
-148.833-148833
4 fs time step Total Energy
Forgot column labels on energies.
Average RMSD
Fluct. Drift Tot-Drift2 fs time step Total Energy
46497.236445.6 2630.7 -148.833-148833
4 fs time step Total Energy41580.837693.42856.08
-13
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