[gmx-users] gmx distance com error

[Debashish Banerjee]

                                    Cs
                                      :
                                      :
                                      :
                                      :
                                      :
                / **************:***********************/
           / ******************:********************/
      /******************************************/

I tried to visualize my problem that I asked. Cs is the atom which I have
fixed at a certain distance from the clay sheet as shown below (containing
192 surface oxygen). I am performing umbrella sampling and using pull code
to pull the particular Cs atom at a given rate in z direction. I just want
to calculate distance of my Cs atom from the center of mass (com) of the
clay sheet as shown above.

Thank you,

Regards,
Debashish

On Thu, May 7, 2020 at 8:51 PM Debashish Banerjee <deb.aerospace at gmail.com>
wrote:

> 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*
>


-- 
*Best Regards*

*Debashish Banerjee*

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