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Eiso AB

  • Registered on: 05/14/2019
  • Last connection: 06/14/2019

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05/25/2019

12:08 AM GROMACS Bug #2954: genion changes residue numbering
waiting for the larger rework sounds fine to me.

05/15/2019

01:31 AM GROMACS Bug #2954: genion changes residue numbering
I've attached files that should allow you to reproduce the problem.
Just put all in one dir and do:...
05:26 PM GROMACS Bug #2953: [ intermolecular_interactions ] with [ distance_restraints ] / [ bonds ] not working
For me, on the system that previously failed, with the fixes, setting nstdisreout=0 or 100 doesn't matter.
It only r...
04:38 PM GROMACS Bug #2954: genion changes residue numbering

Not sure if it is different for this version, but I dont' think it is (or should be) expected behaviour.
There ar...
03:03 PM GROMACS Bug #2953: [ intermolecular_interactions ] with [ distance_restraints ] / [ bonds ] not working
I applied the patches but even with the fix I still need to set -ntmpi 1
(nstdisreout=0)
> You can run with -n...
01:38 PM GROMACS Bug #2953: [ intermolecular_interactions ] with [ distance_restraints ] / [ bonds ] not working
Good,
Pretty sure the label issue is separate (i.e when the label starts from 0 the dis. restr. are still ignored)
...
09:04 AM GROMACS Bug #2953: [ intermolecular_interactions ] with [ distance_restraints ] / [ bonds ] not working

ok, some progress ... I guess it's something with domain decomp
your toy system works fine on one system (deskto...

05/14/2019

11:52 PM GROMACS Bug #2953: [ intermolecular_interactions ] with [ distance_restraints ] / [ bonds ] not working
Berk Hess wrote:
> I tried a toy example with 400 water molecules and a distance restraint between molecules 1 and 2...
03:58 PM GROMACS Bug #2953: [ intermolecular_interactions ] with [ distance_restraints ] / [ bonds ] not working
can you send me the toy example? then I can work from that.
03:48 PM GROMACS Bug #2954 (New): genion changes residue numbering

Using the following commands to add ions:
gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
gmx...

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