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 energy as long as it has been
minimized and has no major clashes.
This is correct, provided T and P coupling are turned off.
Thanks,
Ilya
On Wed, Mar 11, 2009 at 7:38 PM, Ilya Chorny <[email protected]
<mailto:[email protected]>> 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? I thought it might be COM removal so I turned it off to
no avail.
Any chance one of the Gromacs people can give me the mdp file from
the DHFR simulation in the 4.0 paper.
On Tue, Mar 10, 2009 at 10:21 PM, Mark Abraham
<[email protected] <mailto:[email protected]>> wrote:
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
<[email protected] <mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>> 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
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Ilya Chorny Ph.D.
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Ilya Chorny Ph.D.
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