[gmx-users] procedure to measure end-to-end distance of a chain???????

[Rahul Karyappa]

As you told I first created index file by using make_ndx command as
follows ( here I selected group 1 and entered q to save and quit).


There are:  3027      OTHER residues

There are:     1    PROTEIN residues

There are:     0        DNA residues

Analysing Protein...

Analysing Other...


  0 System              :  9369 atoms

  1 Protein             :   288 atoms

  2 Protein-H           :   288 atoms

  3 C-alpha             :     0 atoms

  4 Backbone            :     0 atoms

  5 MainChain           :     0 atoms

  6 MainChain+Cb        :     0 atoms

  7 MainChain+H         :     0 atoms

  8 SideChain           :   288 atoms

  9 SideChain-H         :   288 atoms

 10 Prot-Masses         :   288 atoms

 11 Non-Protein         :  9081 atoms

 12 SOL                 :  9081 atoms

 13 Other               :  9081 atoms


 nr : group       ! 
'name' nr name   'splitch' nr    'l': list
residues

 'a': atom      
&   'del'
nr         'splitres'
nr   'h': help

 't': atom type   |   'keep' nr        'splitat' nr

 'r': residue       
'res': group res 'chain' char    'q': save and quit

 "name": group        'case':
case
sensitive         
'v': verbose output


> 'protein'


Copied index group 1 'Protein'


 14 Protein             :   288 atoms

> q


Then I used g_mindist command to get the end-to-end distance of the polymer chain as follows:


You can compute the distances between a first group

and a number of other groups.

How many other groups do you want (>= 1) ?

1

Group     0 (      System) has  9369 elements

Group     1 (     Protein) has   288 elements

Group     2 (   Protein-H) has   288 elements

Group     3 (     C-alpha) has     0 elements

Group     4 (    Backbone) has     0 elements

Group     5 (   MainChain) has     0 elements

Group     6 (MainChain+Cb) has     0 elements

Group     7 ( MainChain+H) has     0 elements

Group     8 (   SideChain) has   288 elements

Group     9 ( SideChain-H) has   288 elements

Group    10 ( Prot-Masses) has   288 elements

Group    11 ( Non-Protein) has  9081 elements

Group    12 (         SOL) has  9081 elements

Group    13 (       Other) has  9081 elements

Group    14 (     Protein) has   288 elements

Select a group: 1

Selected 1: 'Protein'

Select a group: 1

Selected 1: 'Protein'

Reading frame       0 time    0.000

Back Off! I just backed up mindist.xvg to ./#mindist.xvg.1#

Last frame       1000 time 1000.000


Is this correct or I am doing wrong? PLease help me out.

Thanking you in advance.


Rahul Karyappa

NCL, Pune








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