[gmx-users] g_mindist command doubt???????

[Rahul Karyappa]

Dear all,

   I want to know the  end-to-end distance of my chain
which is surrounded by ions and water molecules. I used g_mindist
command to get the values. But I am confused while selecting the
groups. The following window occurs:


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

1

Reading file topol.tpr, VERSION 3.2.1 (single precision)

Reading file topol.tpr, VERSION 3.2.1 (single precision)

Opening library file /usr/local/gromacs/share/top/aminoacids.dat

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


But how to choose the groups?

Waiting for your kind reply.


Rahul Karyappa

NCL, Pune




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