[gmx-users] suggestion for grompp
nedomacho at gmail.com
Sun Oct 7 04:59:48 CEST 2018
Hi all, and especially the developers!
I've had no success with feature suggestions on redmine, so instead I'll
post here what I think might be a very useful feature, at least for some
As of now, when grompp throws errors about missing bond and angle
parameters, it reports the line in the topology file, in which that
happens. Then one goes into the topology, locates the line, finds the
atom numbers, then determines their types either from the coordinates or
from the atoms section of the topology, then tries fixing the problem.
In my opinion, it is slightly sadistic.
Here is a suggestion: why not have grompp throw the atom type multiplet
in the error message, in addition to the line # in the topology? In
other words, let's say there's a C_type1-C_type2 with missing ffbonded
data. Can you make grompp report that pair, or triplet, or a quadruplet
next to the topology line? This would really make some lives easier and
won't dumb down the process in any way. Sometimes, all it really takes
is copy-pasting that multiplet with the parameters we already know. It's
just incredibly annoying to have to do the lookups manually.
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