Calculating COM for coarse-grained structure

[srdjan125]

Hello,

I am trying to analyze my trajectory from coarse-grained MD trajectory (done by gromacs) and part of my plumed-wham.dat file has following commands:

Dim1: GROUP NDX_FILE=index.ndx NDX_GROUP=DimerA
Dim2: GROUP NDX_FILE=index.ndx NDX_GROUP=DimerB
com1: COM ATOMS=Dim1
com2: COM ATOMS=Dim2
r: DISTANCE ATOMS=com2,com1

I have tried to run the following command:

plumed driver --mf_xtc concatenated.xtc --plumed plumed-wham.dat

However, when I try to run the script I get an error that it cannot compute COM because masses are unknown (obviously because it is coarse grained structure so plumed cannot recognize atom names and their masses).
When I replace it by CENTER (instead of COM) it works, however I want to calculate COM (as during my GROMACS simulations collective variable was distance between COMs).

Is there a way to provide topology info to plumed (for example to provide gromacs tpr file or something).
Thank you in advance.

[GiovanniBussi]

Please check the manual page of driver.

You can use a special command to dump mass and charges with a short MD (DUMPMASSCHARGE) and then read it back in driver (with option --mc).

[srdjan125]

Thank you for answer it worked.