Hi
While trying to find, whats wrong with some of my free energy
calculation, I stumbled upon a strange thing, I don't understand.
I'm simulating the interconversion of ethane to methanol in vacuum.
I'm splitting the process into 3 steps:
1. charge of perturbed atoms -> 0
2. morph of LJ-parameters and bonds
3. charge of perturbed atoms -> B-state values
Each system is morphed with 1 fs timestep and within 50 steps.
The total energies at the "borders" of the simulations (qqoff/vdw,
vdw/qqon, qqon/vdw and vdw/qqoff) perfectly match and show no jump; the
following simulation always got energies and velocities from the one before.
Now, when running the LJ morph A->B with lincs, the dgdl looks like this:
http://www.mpibpc.mpg.de/groups/grubmueller/start/people/mgoette/images/dgdl_lincs_01.png
For B->A:
http://www.mpibpc.mpg.de/groups/grubmueller/start/people/mgoette/images/dgdl_lincs_10.png
Doing both without lincs yields:
http://www.mpibpc.mpg.de/groups/grubmueller/start/people/mgoette/images/dgdl_nolincs_01.png
For B->A
http://www.mpibpc.mpg.de/groups/grubmueller/start/people/mgoette/images/dgdl_nolincs_10.png
I find this spike in the first step extremely strange. Additionally it
only occurs, when using shake or lincs as constraint solver. I guess, in
a longer process it will contribute to the integral in a neglectable
manner, but maybe theres some bug. The latest CVS shows the same behaviour.
Any comments on that?
Regards
--
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.de
WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
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