[gmx-users] Umbrella sampling-gmx distance

Sat Jan 13 16:17:13 CET 2018

Oops,Sorrry. Sometimes big challenges make ones think hard and ignore
obvious issues.
Thank you so much Mr.justin and joao

On Sat, Jan 13, 2018 at 4:01 PM, João Henriques <
joao.m.a.henriques at gmail.com> wrote:

> 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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