[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
value
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
https://www.mail-archive.com/gromacs.org_gmx-users@maillist.sys.kth.se/msg16576.html
https://www.mail-archive.com/gromacs.org_gmx-users@maillist.sys.kth.se/msg30552.html
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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