[gmx-users] Umbrella sampling-gmx distance

[João Henriques]

The output is very explicitly telling you what the problem is. You didn't
provide a topology. Pass one the the -s flag.  How do you want the COM to
be computed when you're not providing any masses?

J

On Jan 13, 2018 9:19 AM, "rose rahmani" <rose.rhmn93 at gmail.com> wrote:

> I'm relly sorry for asking you again and again but...
>
> GROMACS:      gmx distance, VERSION 5.1.4
> Executable:   /usr/local/gromacs/bin/gmx
> Data prefix:  /usr/local/gromacs
> Command line:
>   gmx distance -n index.ndx -f conf0.gro -select 'com of group 2 plus com
> of group 6'
>
>
> -------------------------------------------------------
> Program:     gmx distance, VERSION 5.1.4
> Source file: src/gromacs/trajectoryanalysis/runnercommon.cpp (line 300)
> Function:    void
> gmx::TrajectoryAnalysisRunnerCommon::initTopology(gmx::
> SelectionCollection*)
>
> Inconsistency in user input:
> No topology provided, but one is required for analysis
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> Whai is the problem?;(
>
> On Sat, Jan 13, 2018 at 4:05 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 1/11/18 11:38 AM, rose rahmani wrote:
> >
> >>   [ ZnS ]
> >>     1    2    3    4    5    6    7    8    9   10   11   12   13   14
> >>  15
> >>    16   17   18   19   20   21   22   23   24   25   26   27   28   29
> >>  30
> >>    31   32   33   34   35   36   37   38   39   40   41   42   43   44
> >>   45..............
> >>
> >> [ Protein ]
> >>   761  762  763  764  765  766  767  768  769  770  771  772  773  774
> >> 775
> >>   776  777  778  779  780  781  782  783  784  785  786
> >>
> >> command; gmx distance -n index.ndx -f conf0.gro -select 'com of group
> >> "ZnS"
> >> plus com of group "Protein"' -oxyz -oall
> >> i exactly select index groups!!!
> >> -------------------------------------------------------
> >> Program:     gmx distance, VERSION 5.1.4
> >> Source file: src/gromacs/selection/selectioncollection.cpp (line 616)
> >> Function:    void gmx::SelectionCollection::setI
> >> ndexGroups(gmx_ana_indexgrps_t*)
> >>
> >> Inconsistency in user input:
> >> Invalid index group reference(s)
> >>    Cannot match 'group "ZnS"', because no such index group can be found.
> >>    Cannot match 'group "Protein"', because no such index group can be
> >> found.
> >>
> >> For more information and tips for troubleshooting, please check the
> >> GROMACS
> >> website at http://www.gromacs.org/Documentation/Errors
> >> ------------------------------------------------------------
> >> ---------------------------------
> >> so i had to use this command;  gmx distance -n index.ndx -f conf0.gro
> >> -select -oxyz
> >> GROMACS:      gmx distance, VERSION 5.1.4
> >> Executable:   /usr/local/gromacs/bin/gmx
> >> Data prefix:  /usr/local/gromacs
> >> Command line:
> >>    gmx distance -n index.ndx -f conf0.gro -select -oxyz
> >>
> >> Available static index groups:
> >>   Group  0 "System" (4336 atoms)
> >>   Group  1 "Other" (760 atoms)
> >>   Group  2 "ZnS" (560 atoms)
> >>   Group  3 "WAL" (200 atoms)
> >>   Group  4 "NA" (5 atoms)
> >>   Group  5 "CL" (5 atoms)
> >>   Group  6 "Protein" (26 atoms)
> >>   Group  7 "Protein-H" (12 atoms)
> >> .
> >> .
> >> (one per line, <enter> for status/groups, 'help' for help, Ctrl-D to
> end)
> >>
> >>> 2
> >>>
> >> Selection '2' parsed
> >>
> >>> 6
> >>>
> >> Selection '6' parsed
> >>
> >
> > You should be selecting 'com of group 2' etc. here to get what you want.
> I
> > don't know why the command-line version of this didn't work, but to get a
> > COM distance, you need to tell gmx distance to do it, otherwise it's just
> > going to produce pairwise distances, which is what you're asking for
> here.
> >
> > -Justin
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Assistant Professor
> > Virginia Tech Department of Biochemistry
> >
> > 303 Engel Hall
> > 340 West Campus Dr.
> > Blacksburg, VA 24061
> >
> > jalemkul at vt.edu | (540) 231-3129
> > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
> >
> > ==================================================
> >
> > --
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