[gmx-users] Umbrella sampling-gmx distance

[rose rahmani]

 [ 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
> Reading frames from gro file 'Generated by trjconv : aminoacid-ZnS in
water t=   0.00000', 4336 atoms.
Reading frame       0 time    0.000
Back Off! I just backed up distxyz.xvg to ./#distxyz.xvg.8#
Last frame          0 time    0.000
Analyzed 1 frames, last time 0.000
ZnS:
  Number of samples:  280
  Average distance:   0.52716  nm
  Standard deviation: 0.08068  nm
Protein:
  Number of samples:  13
  Average distance:   0.12566  nm
  Standard deviation: 0.03205  nm

THEN;  vi distxvz.xvg
and again;
 0.000    0.192    0.270    0.191   -0.192   -0.270    0.191    0.383
0.000    0.000    0.383    0.000    0.000    0.383    0.000    0.000
0.383    0.000    0.000    1.131    0.270    0.191    0.382    0.000
0.000    0.382    0.000    0.000    0.383    0.000    0.000    0.383
0.000    0.000    0.383    0.000    0.000    0.383    0.000    0.000
0.383    0.000    0.000    0.382    0.000    0.000    0.748   -0.270
0.191    0.382    0.000    0.000    0.382    0.000    0.000    0.382
0.000    0.000    0.382    0.000    0.000    0.000    0.541    0.000
0.000    0.541    0.000   .............


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