[gmx-users] Re: Energy Drift in Gromacs 4.0
Mark.Abraham at anu.edu.au
Wed Mar 11 06:21:52 CET 2009
Ilya Chorny wrote:
> Forgot column labels on energies.
> RMSD Fluct. Drift Tot-Drift
> 2 fs time step Total Energy 46497.2 36445.6 2630.7
> -148.833 -148833
> 4 fs time step Total Energy 41580.8 37693.4 2856.08
> -130.198 -130198
> On Tue, Mar 10, 2009 at 7:17 PM, Ilya Chorny <ichorny at gmail.com
> <mailto:ichorny at gmail.com>> wrote:
> Hello All,
> I am trying to run some calibration calculations with 2/4 fs time
> steps. I am trying to reproduce the results in the Gromacs 4.0 paper
> on a protein/water (not the same protein) system with ~100K atoms. I
> ran 1 ns simulation in the NVE ensemble. My mdp params are shown
> below. Topolgy was created using -vsite h. My system has 218441
> degrees of freedom according to GMXDUMP. My P.E. energy is ~ -1E5
> and has not full relaxed after 1ns but is close.
> 2 fs time step Total Energy 46497.2 36445.6
> 2630.7 -148.833 -148833
> 4 fs time step Total Energy 41580.8 37693.4
> 2856.08 -130.198 -130198
> Drift (kt/ns) 2fs/4fs = .34/.29
> The drift seems to be much larger for both the 2fs and 4fs time
> steps then in the paper. Do I have a clear bug in my params? Should
> I wait till the system fully relaxes before doing the drift calculation?
You should definitely equilibrate the system before trying to measure
energy drift. I suggest doing so in NPT to fix your density and
temperature, then switching to NVE, wait a bit, and only then start to
collect your data.
> coulombtype = PME
> rcoulomb = 1.0
> fourierspacing = 0.12
> ; FFT grid size, when a value is 0 fourierspacing will be used
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> ; EWALD/PME/PPPM parameters
> pme_order = 4
> ewald_rtol = 1.e-04
I would think the ewald_rtol value used in the paper was 1e-5, but it is
unfortunately not stated. The different numbers will lead to different
costs and accuracies for the direct and FFT parts of the PME algorithm.
rcoulomb, fourier_whatever, pme_order and ewald_rtol are all relevant if
you're trying to reproduce results.
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