[gmx-users] gmx distance

[Deva Priya]

Hello Teemu,

Thanks for your response. I updated to GMX 5.1 and tried to use gmx
pairdist.

There are few examples of using pairdist correctly. So, please forgive my
question.

I tried to specify "name K" and on the second option, "com of group 13".
This results in a distance file, which I am not sure is what I want.

Do I need to specify each atom number of K with com of group 13 and then
average the distances? or is there an easier way to do this? I have 97 K
atoms in my simulation.

Thanks again for your help.

Deva


On Mon, Oct 19, 2015 at 12:40 AM, Teemu Murtola <teemu.murtola at gmail.com>
wrote:

> No, this does not calculate what you want. If you had an even number of K
> atoms, it would even refuse to calculate. What you get is the distance
> between the first and second K, third and fourth K, and so on, and finally
> between the last K and the com.
>
> You can get the individual distances with gmx pairdist (from Gromacs 5.1),
> and average them yourself.
>
> Best regards,
> Teemu
>
> On Mon, Oct 19, 2015, 00:53 Deva Priya <devapriyachem at gmail.com> wrote:
>
> > I think I figured it out.
> >
> > It should be selected as "name K plus com of group XX". Running the
> command
> > with -oall confirms that it calculates distance for each atom with name K
> > and com of other group.
> >
> > I would still appreciate any comment, if this is a faulty solution.
> >
> > Thanks,
> >
> >
> > On Sun, Oct 18, 2015 at 4:42 PM, Deva Priya <devapriyachem at gmail.com>
> > wrote:
> >
> > > Hello,
> > >
> > > I am trying to set up a calculation to measure distance between the
> > > following groups.
> > >
> > > group A = center of mass of a selection of atoms
> > > group B = atoms of another group (all K atoms)
> > >
> > > Is it possible to specify the command such that the distance output is
> > the
> > > average distance between group A and each atom of group B. So, the
> answer
> > > could be reported as average distance between all K atoms and center of
> > > mass of group B.
> > >
> > > Any advice is greatly appreciated.
> > >
> > > Thanks,
> > > Deva
> > >
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>