John D.
Activity
10/20/2007
- 10:13 AM GROMACS Bug #172: incorrect handling of angle bending leads to errors for obtuse angles and crashes for angles of 180
- Thanks for the quick diagnosis and fix, David!
You're right -- I had missed the rectification conditions to ensure t... - 08:11 AM GROMACS Bug #124: Distribution of instantaneous kinetic temperature generated by Nose-Hoover appears to be incorrect
- Berk,
Thanks for tracking down the cause of the deviation! I'd agree that a weakly-interacting dilute gas could pos...
10/17/2007
- 07:25 PM GROMACS Bug #172: incorrect handling of angle bending leads to errors for obtuse angles and crashes for angles of 180
- Hi guys,
Could you simply use double-precision accumulators for the computation of cos_theta and acos(cos_theta)? I... - 07:24 PM GROMACS Bug #124: Distribution of instantaneous kinetic temperature generated by Nose-Hoover appears to be incorrect
- Hi Berk,
It's in there! In data/, you can find the .mdp, .gro, and .top files for each test in the test subdirector... - 10:13 AM GROMACS Bug #124: Distribution of instantaneous kinetic temperature generated by Nose-Hoover appears to be incorrect
- Created an attachment (id=252)
Test setup for the 500 particle LJ thermostat test.
Berk,
Sorry for taking so long t... - 10:06 AM GROMACS Bug #124: Distribution of instantaneous kinetic temperature generated by Nose-Hoover appears to be incorrect
- Created an attachment (id=251)
Histogram of instantaneous kinetic temperatures for Langevin integrator and Nose-Hoove... - 09:08 AM GROMACS Bug #172: incorrect handling of angle bending leads to errors for obtuse angles and crashes for angles of 180
- Created an attachment (id=250)
propyne in vacuum test case from David Mobley.
Added propyne in vacuum test case from... - 08:59 AM GROMACS Bug #172: incorrect handling of angle bending leads to errors for obtuse angles and crashes for angles of 180
- As far as my meagre brain can grasp, the angle energy terms and gradient are computed in gmxlib/bondfree.c, in a func...
10/04/2007
- 10:31 AM GROMACS Bug #124: Distribution of instantaneous kinetic temperature generated by Nose-Hoover appears to be incorrect
- (In reply to comment #10)
> I looked again at the file I downloaded from your site
> and now realized that the print ... - 09:53 AM GROMACS Bug #124: Distribution of instantaneous kinetic temperature generated by Nose-Hoover appears to be incorrect
- (In reply to comment #8)
> You used Berendsen pressure coupling!!!
>
> When I turned that on I got the peak.
>
> A ...
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