Hi, all-
At this point, any fixes are going to be in the 5.0 version, where the
integrators will be a bit different. If you upload your system files
to redmine.gromacs.org (not just the .mdp), then I will make sure this
gets tested there.
On Fri, Oct 25, 2013 at 10:14 AM, Guillaume Chevrot
wrot
Dear Xavier,
2013/10/12 XAvier Periole
>
> Could you try to reduce the nstcalcenergy flag from 100 to 10 and then one?
>
>
FYI, I tried 10 and 1 and the energy drift is exactly the same.
> Similar flags apply to temperature and pressure and I believe might
> seriously affect energy conserva
On Sat, Oct 12, 2013 at 11:07 PM, Guillaume Chevrot <
guillaume.chev...@gmail.com> wrote:
> 2013/10/12 Mark Abraham
>
> > Didn't see any problem in the .mdp. -4500 kJ/mol in 10ns over (guessing)
> > 30K atoms is 0.015 kJ/mol/ns/atom. k_B T is at least 100 times larger
> than
> > that. I bet the r
2013/10/12 XAvier Periole
>
> Could you try to reduce the nstcalcenergy flag from 100 to 10 and then one?
>
>
Thanks for the suggestion. I'll try next week and I'll show the results
ASAP.
Guillaume
> Similar flags apply to temperature and pressure and I believe might
> seriously affect ene
2013/10/12 Mark Abraham
> Didn't see any problem in the .mdp. -4500 kJ/mol in 10ns over (guessing)
> 30K atoms is 0.015 kJ/mol/ns/atom. k_B T is at least 100 times larger than
> that. I bet the rest of the lysozyme model physics is not accurate to less
> than 1% ;-) There are some comparative num
Could you try to reduce the nstcalcenergy flag from 100 to 10 and then one?
Similar flags apply to temperature and pressure and I believe might seriously
affect energy conservation.
XAvier.
> On Oct 12, 2013, at 0:50, Mark Abraham wrote:
>
> Didn't see any problem in the .mdp. -4500 kJ/mo
Didn't see any problem in the .mdp. -4500 kJ/mol in 10ns over (guessing)
30K atoms is 0.015 kJ/mol/ns/atom. k_B T is at least 100 times larger than
that. I bet the rest of the lysozyme model physics is not accurate to less
than 1% ;-) There are some comparative numbers at
http://dx.doi.org/10.1016/
Hi,
sorry for my last post! I re-write my e-mail (with some additional
information) and I provide the links to my files ;-)
I compared the total energy of 2 simulations:
lysozyme in water / NVE ensemble / single precision / Gromacs 4.6.3
lysozyme in water / NVE ensemble / double precision / Groma
On Oct 11, 2013 7:59 PM, "Guillaume Chevrot"
wrote:
>
> Hi all,
>
> I recently compared the total energy of 2 simulations:
> lysozyme in water / NVE ensemble / single precision
> lysozyme in water / NVE ensemble / double precision
>
> ... and what I found was quite ... disturbing (see the attached
Hi, Guillaume-
No one can tell you if you did anything wrong if you didn't tell us
what you did! There are literally thousands of combinations of
options in running an NVE simulation, a substantial fraction of which
are guaranteed not to conserve energy.
If you post the files (inputs and relevan
Hi all,
I recently compared the total energy of 2 simulations:
lysozyme in water / NVE ensemble / single precision
lysozyme in water / NVE ensemble / double precision
... and what I found was quite ... disturbing (see the attached figure -
plots of the total energy). I observe a constant drift in
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