Ilya Chorny wrote:
Forgot column labels on energies.
Average
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 <icho...@gmail.com
<mailto:icho...@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.
Mark
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
