[gmx-users] Umbrella sampling-gmx distance

[rose rahmani]

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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