Where does gmx insert-molecules read masses and radii?

User discussions
1

GROMACS version: 2020.3
GROMACS modification: No
Hello,

I was wondering where does gmx insert-molecules search for atoms mass and radius.
I have some solid particles I am simulating and the initial configuration I am generating with gmx insert-molecules, but I get this warning:

WARNING: Masses and atomic (Van der Waals) radii will be guessed
based on residue and atom names, since they could not be
definitively assigned from the information in your input
files. These guessed numbers might deviate from the mass
and radius of the atom type. Please check the output
files if necessary.

I already have a modified at atommass.dat and vdwradii.dat that include my new particles, I modified the files in the working directory not in the gromacs installation folder. Should I change in the installation or this program reads these data from other file?

Thank you so much!
Cintia

2

The warning is always printed if the input file is not a .tpr file, i.e. in the absence of any actual topological information. The values are taken from atommass.dat and vdwradii.dat. The program is just telling you that there is a possibility that something weird is going on. For instance, is CA a carbon or is it calcium, is HG a hydrogen or mercury? For the purpose of insert-molecules the distinctions are likely of minimal importance, but the warning is a generic feature of different programs that need such information and can’t necessarily get it from coordinate files.

1 Like
3

I’m wondering if you can specify the location of the atommass.dat and vdwradii.dat files (i.e. within the working directory) instead of using the installed Gromacs files?

I’m running my programs on a computing cluster and don’t have access to modify the Gromacs install.

Thanks!

4

All GROMACS programs will read relevant database files from the working directory before referencing them from $GMXLIB.