[gmx-developers] head mdrun broken?
mrshirts at gmail.com
Thu Dec 24 17:14:51 CET 2009
> The initial temperature with integrators md and sd is exactly
> a factor of 2 too low, I guess currently the average ekin of
> a correct number and 0 is taken.
This is correct. I didn't notice before, since the .edr temperatures
are all correct, just not the initial temperature printed to the log.
I've put in a simple fix for now (bit of a kludge, I just multiply by
two, but it's simpler than messing with the complicated logic of
temperature calculation that needs to handle three integrators . . .
> Berendsen pcoupl works with md, but with sd the box is nan
> after the second neighbor search step.
I think this was fixed by a patch I put in last night; please let me
know if you're still getting a bug, and This bug emphasized the need
for good coding practices -- there was a one-line conditional without
brackets that I missed when I was adding velocity verlet. If it had
brackets, I would have noticed it the first time and save a couple
hours of debugging :)
Thanks for all the error reports -- keep them coming! Unless,
hopefully, there aren't any more!
> Michael, could you look into this?
>> After some further checks I noticed that I now get infinite energies in a
>> simple system with the sd integrator (which didn't happen before).
>> I'll send you the run files off-list.
>> On Dec 22, 2009, at 18:19 , Michael Shirts wrote:
>>>> And Berendsen pressure coupling fails with a segv in pme.c - calc_idx
>>>> because of NaNs in the reciprocal box size..
>>> Berendsen seems to be working OK for me. Sander, could you send me
>>> your .mdp so I can make sure I'm covering all the options?
>>> Obviously, my test cases before submitting are not broad enough! :)
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