GROMACS development

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 ...