[gmx-users] suggestion for grompp

Alex 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 
of us.
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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