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Bug #1061

MTTK conserved energy is drifting

Added by Shun Sakuraba about 5 years ago. Updated almost 5 years ago.

Status:
Closed
Priority:
Normal
Assignee:
Category:
mdrun
Target version:
-
Affected version - extra info:
4.5.5
Affected version:
Difficulty:
uncategorized
Close

Description

When I used MTTK integrator, the conserved energy (not total energy) of MTTK is drifting during the simulation.
It is drifting with a constant ratio of ca. -185 kJ/mol/ps.
The drift is caused even when I use the double precision version, and switching potential, and 0.5 fs time-step.
Although the fluctuation in the conserved energy is possible by nature of MTTK equation, constant drift during the full simulation time is not what I expect.
The problem is reproduced with either gcc 4.6.1 or icc 11.1.

Reproduce procedure:
grompp_d -f mpt-mttk05.mdp -c conf.gro -p spce.top -o mttk
mdrun_d -deffnm mttk

npt-mttk05.mdp (558 Bytes) npt-mttk05.mdp Simulation condition Shun Sakuraba, 12/06/2012 05:29 AM
conf.gro (202 KB) conf.gro Initial configuration (prepared with Berendsen barostat) Shun Sakuraba, 12/06/2012 05:29 AM
spce.top (102 Bytes) spce.top Topology Shun Sakuraba, 12/06/2012 05:29 AM
mttk05.xvg (779 KB) mttk05.xvg Plot of energy drifting Shun Sakuraba, 12/06/2012 05:29 AM

Associated revisions

Revision b18b7833 (diff)
Added by Michael Shirts almost 5 years ago

Fix for the pressure in MTTK with constraints + dispersion

Fix for pressure in MTTK - broken at some point in the
merge process. The MTTK+constraints code definitely needs to
be simplified for 5.0, it's too easy to break on code rearrangements
right now!

Testing with simple systems over long time shows that the pressure is
unbiased, while the PR pressure is off by a factor of 1/N (which is totally
fine for most realistic systems).

Fixes redmine bug #1061
Change-Id: Ie82cf8d6bdeb3e47db044ae34fc42c077ad73c75

Revision 66cab279 (diff)
Added by Mark Abraham almost 5 years ago

New reference files for freeenergy/relative

The code version includes Berk's LINCS fix
https://gerrit.gromacs.org/1940, and Michael's MTTK fix
https://gerrit.gromacs.org/1859

Refs #1061

Change-Id: I5791bf2fb5f9e02b41d4a3543b9f0a6489f546f1

History

#1 Updated by Michael Shirts about 5 years ago

  • % Done changed from 0 to 100

OK, the commit submitted to 4.6 appears to fix this:

https://gerrit.gromacs.org/#/c/1859/

You can check it out -- in a run out to 16 ps. the conserved quantity has stayed within 10 kJ/mol from the total energy, as it should, and is not drifting up -- in the .xvg above, it had dropped 2000 kJ/mol by this point in the code.

When 4.6 is out, I'll go back and figure out the proper changes to backport to 4.5-patches.

#2 Updated by Erik Lindahl almost 5 years ago

  • Status changed from New to Closed

Fixed in git by Michael's revision b18b7833.

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