Printing COM distances between two COM groups produces nan

[billy.willi...@gmail.com]

Hi there Plumed experts,

I am using the following plumed input entitled plumed-print-distance.dat:

com1: COM ATOMS=1-3
com2: COM ATOMS=64-67

d1: DISTANCE ATOMS=49,25
d2: DISTANCE ATOMS=5,49
d3: DISTANCE ATOMS=44,36
d4: DISTANCE ATOMS=2,64

PRINT STRIDE=1 ARG=d1,d2,d3,d4 FILE=All_dist_thin

And the following plumed command:

plumed driver --plumed plumed-print-distance.dat --mf_trr ./meta_thin.trr --trajectory-stride 1

And it produces nan for the CV labeled 'd4'.

Both the COLVAR file and the HILLS file from the original GROMACS trajectory include values for 'd4'.  But when I try and print the distances with plumed driver using the same pre-defined CVs it will not produce a number for 'd4'.

Any help on the correct syntax to use to print these distances would be appreciated.

Kind regards,

Billy

[billy.willi...@gmail.com]

I've read here that:

Notice that by default the driver has no knowledge about the masses and charges of your atoms! Thus, if you want to compute quantities depending charges (e.g. DHENERGY) or masses (e.g. COM) you should pass the proper information to the driver. You can do it either with the –pdb option or with the –mc option. The latter will read a file produced by DUMPMASSCHARGE.

Could someone please point me in the right direction about how to use the -pdb option?

[Giovanni Bussi]

You should put masses in the occupancy field of the PDB.

Notice that PDB have a fixed column format that might be error prone. My recommendation is to run a short (1 step) md using DUMPMASSCHARGE to produce a mass/charge file then read it back from the driver command line with "--mc". See the example on the DUMPMASSCHARGE documentation.

Giovanni

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