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

leafyoung81-group at yahoo.com leafyoung81-group at yahoo.com
Wed Sep 14 12:11:51 CEST 2005

you need to define a new .ndx which include the no. for the atoms. feed this .ndx file to g_mindist or g_bond with -n option.
Yang Ye
Rahul Karyappa <r.karyappa at ncl.res.in> wrote:

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) ?
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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