[gmx-users] Why do g_trjconv and g_select give different results for the same cut-off

Mark Abraham mark.j.abraham at gmail.com
Tue Jun 12 16:48:47 CEST 2018


"number of molecules within the cutoff" is not yet well defined. You could
say that any atom of any appropriate molecule being within the cutoff is
good enough. Or all atoms from molecules. Or the center of mass of the
molecules. So the default mode for any tool might be different.

Check out the docs for the two tools, and make sure you've made choices
that match what you actually want, or so that you can compare apples with
apples. (The implementations are different, so you will not get 100%
agreement for every frame, but you should be able to get it pretty close
with choices that actually match.)


On Tue, Jun 12, 2018 at 11:48 AM Apramita Chand <apramita.chand at gmail.com>

> Dear All,
> When I use g_select,on giving the command,
> g_select -select ' resname UREA and within 0.45 of group Backbone' -f
> 100nc_entire.xtc -s md.tpr -os size_within0.45_urea_backbone.xvg -oi
> index_within0.45_urea_backbone.dat -oc cfrac_urea_within0.45_backbone.xvg
> -seltype mol_com
>  it gives me an average of 9-10 solute molecules around reference protein.
>  But when I use g_trjorder , I get 20-23 molecules on an average for the
> same cut-off of 0.45nm.
> Any reason why this might be happening?
> Thanks,
> Yours sincerely,
> Apramita Chand
> --
> 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.

More information about the gromacs.org_gmx-users mailing list