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Flaviyan Jerome Irudayanathan

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11/30/2017

03:42 PM GROMACS Feature #2310: Let mdrun dump coordinates with non-finite energy
Hi Berk,
Yes this would be useful feature.
For my current case I think i am fine as one of the duplicates did no...

11/29/2017

06:33 PM GROMACS Feature #2310: Let mdrun dump coordinates with non-finite energy
Aleksei Iupinov wrote:
> Suggest attaching input files/command line
Hi Aleksei,
The simulation is a replica ex...

11/28/2017

09:49 PM GROMACS Feature #2310 (Accepted): Let mdrun dump coordinates with non-finite energy
Hi,...

10/10/2017

12:46 AM GROMACS Bug #2268: v-site construction ignore water fails for charmm force filed
Hi David and Berk,
This is my understanding so far kindly correct me if i am wrong:
while constructing virtual ...
10:51 PM GROMACS Bug #2268: v-site construction ignore water fails for charmm force filed
Not sure if all force-fields have atom numbers
I compiled this:...
09:35 PM GROMACS Bug #2268: v-site construction ignore water fails for charmm force filed
Yes in charmm27 lipids have the OH2 name. I can't find non-water OH2 in charmm36.
08:41 PM GROMACS Bug #2268: v-site construction ignore water fails for charmm force filed
Sorry my report wasn't clear.
I agree with you water is not handled by the vsite code,
if I provide an input file w...
04:35 PM GROMACS Bug #2268 (Closed): v-site construction ignore water fails for charmm force filed
The ignore water logic in gen_vsite.cpp checks if the heavy atom name is "OW"
and skips the waters in the input file...

04/28/2017

08:46 PM GROMACS Task #2166 (Accepted): gmx trjconv functionality should check for mismatch between the tpr and the trajectory
this happens in both 5.1.4 and 2016.3
system1 and system2 have different number of atoms and different molecules....

05/20/2016

07:18 PM GROMACS Feature #1966: Hydrogen mass repartiniong
I looked into the -viste option, Thanks for the suggestions.
I guess this ticket can be closed then.

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