RE: [gmx-users] Re: Energy Drift in Gromacs 4.0

2009-03-12 Thread Berk Hess
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

[gmx-users] Re: Energy Drift in Gromacs 4.0

2009-03-12 Thread Luca De Gaetani
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

Re: [gmx-users] Re: Energy Drift in Gromacs 4.0

2009-03-11 Thread David van der Spoel
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

Re: [gmx-users] Re: Energy Drift in Gromacs 4.0

2009-03-11 Thread Mark Abraham
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?

Re: [gmx-users] Re: Energy Drift in Gromacs 4.0

2009-03-11 Thread Ilya Chorny
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

Re: [gmx-users] Re: Energy Drift in Gromacs 4.0

2009-03-11 Thread Ilya Chorny
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

Re: [gmx-users] Re: Energy Drift in Gromacs 4.0

2009-03-10 Thread Mark Abraham
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

[gmx-users] Re: Energy Drift in Gromacs 4.0

2009-03-10 Thread Ilya Chorny
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