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João M. Damas

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04/01/2015

05:53 AM GROMACS Feature #1688: g_cluster "middle" is not exactly the same as the definition in the cited paper
I agree with Chris. My suggestion would be to output the Daura's "center of cluster" to stderr as a warning for when ...

03/04/2014

11:35 PM GROMACS Bug #1449: g_sas computes incorrect values with "-pbc yes"
Hello Teemu,
You are right. I had a small bug in my batch script when I ran the version with the bigger box, which...
07:00 PM GROMACS Bug #1449: g_sas computes incorrect values with "-pbc yes"
I am sorry, I have not provided the files where I used editconf -d 5 in between pdb2gmx and grompp. I provide those n...
05:53 PM GROMACS Bug #1449: g_sas computes incorrect values with "-pbc yes"
So, these files were obtained from the ATOM records of the .pdb structures (taken from the PDB), through the standard...
05:39 PM GROMACS Bug #1449: g_sas computes incorrect values with "-pbc yes"
To prevent misinterpretations, I did not attribute any assignee when I filed this issue.
05:04 PM GROMACS Bug #1449 (Rejected): g_sas computes incorrect values with "-pbc yes"
g_sas is computing incorrect surface areas when PBC is being considered ("-pbc yes").
This is a lingering problem ...
04:57 AM GROMACS Bug #1445: g_sas computes incorrect values with -nopbc
Teemu Murtola wrote:
> Applied in changeset commit:a56228accb8dc04c7ef08fe6bfc7518da43c218d.
Conclusion on this i...

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