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

[Tsjerk Wassenaar]

Hi Rahul,

Make an index file with two groups: 

[ CTERM ]
1
[ NTERM ]
288

and use that with g_mindist.

Cheers,

Tsjerk

On 9/14/05, 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) ?
> 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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-- 
Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciencesand Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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