How to write the trajectory file using center of mass of each molecule?

User discussions
1

My MD system is composed of cations, anions and water residues where each type has 500 molecules, a total of 1500 molecules in the system. A cation molecules has 20 atoms, an anion molecules has 15 atoms and for the water molecule it has 4 atoms (I am using tip4p-2005 water model). I want to write a trajectory file separately for each residues type for the calculation of velocity auto-correlation function. In the trajectory file, at each time frame, I would like to write the center of mass velocities for each molecule.

To do so I wrote the following command:

gmx_mpi traj -f md.trr -s md.tpr -n index.ndx -ov traj-wat.xvg -com -mol

and then choose the group for water

However, I am getting this error,

Fatal error:
Molecule index (17501) is out of range (1-1500)

I also tried the “splitres” command while making the index file, in which make_ndx is creating sperate groups for each molecule. However, even after using this index file, I am getting the same error as above.

Below is the clip from index file where “splitres” command is used for water molecules:

[ Water_SOL_1005 ]
17517 17518 17519 17520
[ Water_SOL_1006 ]
17521 17522 17523 17524
[ Water_SOL_1007 ]
17525 17526 17527 17528
[ Water_SOL_1008 ]
17529 17530 17531 17532
[ Water_SOL_1009 ]
17533 17534 17535 17536
[ Water_SOL_1010 ]
17537 17538 17539 17540
[ Water_SOL_1011 ]
17541 17542 17543 17544
[ Water_SOL_1012 ]
17545 17546 17547 17548
[ Water_SOL_1013 ]
17549 17550 17551 17552
[ Water_SOL_1014 ]
17553 17554 17555 17556
[ Water_SOL_1015 ]
17557 17558 17559 17560

Can someone please help in resolving this issue.

Thank You

Priya Yadav

2

When you use the -mol option, you should provide indices of molecules, not of atoms.

3

Dear, thank you for your reply.

I am not able to get how to provide the indices for molecules instead of atoms. In the .gro (.trr/.tpr) file it has both the atom and molecule indices.