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David Mobley

  • Email: dmobley@uci.edu
  • Registered on: 04/30/2013
  • Last connection: 02/02/2015

Issues

Activity

03/19/2015

10:57 PM GROMACS Bug #1648: Atoms with zero LJ parameters but partial charges appear to cause crashes in free energy calculations when perturbed in the presence of other charges
To update on this, we were able to reduce the system to a couple of benzoic acid molecules in gas and still get crash...

02/11/2015

07:47 PM GROMACS Bug #1648: Atoms with zero LJ parameters but partial charges appear to cause crashes in free energy calculations when perturbed in the presence of other charges
I have reproduced my student's work and verified that the issue disappears if the hydroxyl hydrogen LJ parameters are...

02/09/2015

06:39 PM GROMACS Bug #1684 (Closed): Issue 1648 also applies to 5.0.4
Not sure if this is the right way to flag this, but I wanted to report that issue 1648 (http://redmine.gromacs.org/is...
06:35 PM GROMACS Bug #1648: Atoms with zero LJ parameters but partial charges appear to cause crashes in free energy calculations when perturbed in the presence of other charges
I have now reproduced this problem in 5.0.4 with a somewhat simpler protocol. In this case I'm running without constr...

02/02/2015

07:05 PM GROMACS Bug #1648: Atoms with zero LJ parameters but partial charges appear to cause crashes in free energy calculations when perturbed in the presence of other charges
I have verified all of these issues still persist for me both in the git has referenced above, and with the released ...

11/26/2014

06:33 PM GROMACS Bug #1648: Atoms with zero LJ parameters but partial charges appear to cause crashes in free energy calculations when perturbed in the presence of other charges
Berk - yes, I should have full LJ, which is why it's so peculiar it's crashing and that addition of LJ parameters to ...
05:24 AM GROMACS Bug #1648: Atoms with zero LJ parameters but partial charges appear to cause crashes in free energy calculations when perturbed in the presence of other charges
All lambdas crash except #0, though the amount of time is variable. All of them make it into production except one. T...
02:14 AM GROMACS Bug #1648 (Feedback wanted): Atoms with zero LJ parameters but partial charges appear to cause crashes in free energy calculations when perturbed in the presence of other charges
I've run several systems now with free energy calculations where I run into crashes whenever I perturb a molecule hav...

06/25/2014

10:37 PM GROMACS Bug #1457: Bug(s) relating to intermolecular_interactions section, harmonic 'bonds' (type 6) for v5
Ah, indeed, there is a typo (distance restraint applied to 1410-2610 rather than 1410-2601 as it ought to be) in the ...

03/07/2014

08:40 PM GROMACS Bug #1457 (Closed): Bug(s) relating to intermolecular_interactions section, harmonic 'bonds' (type 6) for v5
We have been testing protein-ligand restraints in GROMACS 5.0-beta2-dev-20131228-39aa759, from https://gerrit.gromacs...

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