[gmx-users] gmx distance com error

Debashish Banerjee deb.aerospace at gmail.com
Thu May 7 20:51:44 CEST 2020

Hello gmx users,

I am stuck at a very basic command line and need your expertise in dealing
through it.

Basically, I have a clay sheet containing 192 surface oxygen. Since I am
doing umbrella sampling for PMF calculations, I want to get the progression
of COM distances of my fixed Cs atom from the center of mass of the clay
sheet (basically these 192 surface oxygen) over time.

I have already created special index file which has relevant groups such as
group 18 --> *referenceSurface* ~containing 192 surface oxygen
group 19 --> *restrainedCs* ~containing 1 Cs atom (basically the one that I
have fixed)
group 20 --> another Cs atom (this one is not fixed and can move freely in
all sample space during the entire course of simulation)

Command line:

*Case 1*

*gmx_mpi distance -n index.ndx -f conf0.gro -s pull.tpr -select 'com of
group 19 plus com of group 18' -oxyz dist00.xvg*

Inconsistency in user input:
Invalid index group reference(s)
  Group 'referenceSurface' cannot be used in selections except as a full
  of the selection, because atom indices in it are not sorted and/or it
  contains duplicate atoms.

*Case 2*
*gmx_mpi distance -n index.ndx -f conf0.gro -s pull.tpr -select 'com of
group 19 plus com of group 20' -oxyz dist2.xvg*

Reading file npt.tpr, VERSION 2016.4 (single precision)
Reading frames from gro file 'Generated by trjconv : clay + Cs + acetate +
water t=   2.00000', 24221 atoms.
Last frame          0 time    2.000
Analyzed 1 frames, last time 2.000
com of group 19 plus com of group 20:
 Number of samples:  1
 Average distance:   0.52370  nm
 Standard deviation: 0.00000  nm

My understanding is that if I compare the above 2 cases, I would say that
for *case 2*, Cs is measuring it's distance from the only other Cs atom. No
problem here, whereas for *case 1*, Cs atom is measuring it's distance from
all 192 oxygen atoms, somehow not understanding how to take the center of
mass of the whole sheet containing 192 atoms.

Approach taken:
1. Modified my command line from this:
 gmx_mpi distance -s pull.tpr -f conf0.gro -n index.ndx -select 'com of
group "restrainedCs" plus com of group "referenceSurface"' -oall dist0.xvg
2. Used all output options like -oav / -oxyz

I have followed the following threads, but still couldn't manage to rectify
this error


Please help. I am pretty much sure that I am overseeing a very basic step.

*Best Regards*

*Debashish Banerjee*

*Ph.D. (Nuclear Materials, Subatech)*
*MS(Sustainable Nuclear Engineering)*
*Advance Nuclear Waste Management*
*Institut Mines-Telecom, **France*

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