Dear Xavier,
2013/10/12 XAvier Periole x.peri...@rug.nl
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
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
On Sat, Oct 12, 2013 at 11:07 PM, Guillaume Chevrot
guillaume.chev...@gmail.com wrote:
2013/10/12 Mark Abraham mark.j.abra...@gmail.com
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
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 mark.j.abra...@gmail.com wrote:
Didn't see any problem in
2013/10/12 Mark Abraham mark.j.abra...@gmail.com
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
2013/10/12 XAvier Periole x.peri...@rug.nl
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
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
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
On Oct 11, 2013 7:59 PM, Guillaume Chevrot guillaume.chev...@gmail.com
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
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 /
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
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