[gmx-users] Error in calculating center of mass using distance command

[Jorden Cabal]

Hi Sumedha,
I think you are using the default value of -len (i.e Mean distance for
histogramming) in the command which is 0.1. If you data points contains
distance values which has larger mean than this, histogramming for those
values will not be calculated. For conformation, you can check the output
file, you will see that it ends 0.2. I hope this might help you.
Thanks

On Wed, Aug 21, 2019 at 10:54 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 8/21/19 9:52 AM, Sumedha Bhosale wrote:
> > Hello,
> >
> > I am trying to calculate the center of mass of residues 513-515 and
> 588-590
> > of chain A and chain B using distance command. I want output in histogram
> > format. But it seems that distance command is a calculating the distance
> of
> > my first group and itself. It's not taking the second group. I am getting
> > all values as zero in histogram plot.
> > I have made index files for two separate groups of chain A and chain B. I
> > am using the command - com of group 34 plus com of group 35.
>
> Please provide the exact command you gave, directly copied and pasted
> from the terminal.
>
> -Justin
>
> --
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> Justin A. Lemkul, Ph.D.
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