[gmx-users] Problem with g_rdf

Hector Manuel Manzanilla Granados hmanzanilla at ipn.mx
Wed Feb 20 06:46:11 CET 2013

Excuseme dear Dr. Tomas, forgiveme the boldness,
I'm new with this, and I dont know who to address
when I have a problem. My name is Hector, and  I'm
tryng to install the gromacs software in my computer;
I follewed all the steps in the online manual, however
when I compile Gromacs with the instruction: ngmx, I receiveç
the following sentence:

:-)  G  R  O  M  A  C  S  (-:

            Glycine aRginine prOline Methionine Alanine Cystine Serine

                             :-)  VERSION 4.0.7  (-:

       Written by David van der Spoel, Erik Lindahl, Berk Hess, and 
        Copyright (c) 1991-2000, University of Groningen, The 
              Copyright (c) 2001-2008, The GROMACS development team,
             check out http://www.gromacs.org for more information.

          This program is free software; you can redistribute it 
           modify it under the terms of the GNU General Public License
          as published by the Free Software Foundation; either version 
              of the License, or (at your option) any later version.

                                  :-)  ngmx  (-:

Option     Filename  Type         Description
   -f       traj.xtc  Input        Trajectory: xtc trr trj gro g96 pdb 
   -s      topol.tpr  Input        Run input file: tpr tpb tpa
   -n      index.ndx  Input, Opt.  Index file

Option       Type   Value   Description
-[no]h       bool   no      Print help info and quit
-nice        int    0       Set the nicelevel
-b           time   0       First frame (ps) to read from trajectory
-e           time   0       Last frame (ps) to read from trajectory
-dt          time   0       Only use frame when t MOD dt = first time 

Program ngmx, VERSION 4.0.7
Source code file: ../../../../src/gmxlib/gmxfio.c, line: 737

Can not open file:

"It's Calling Me to Break my Bonds, Again..." (Van der Graaf)

I don't understand what to do with this, may be you can get me a hint,

thank you very much and excuse me.

Best regards.

On Tue, 19 Feb 2013 23:04:48 +0100
  Thomas Schlesier <schlesi at uni-mainz.de> wrote:
> On 2/19/13 3:10 PM, Thomas Schlesier wrote:
> > Dear all,
> > I have a question regarding g_rdf.
> > My system consits of 10 disacchardids (in the following A-B, with
> > A-ring/monosaccharid and B-ring/monosaccharid) and i want to 
>determine the RDF
> > (with flag '-rdf mol_com')for A-A, B-B and the intermolekular for 
> >
> > A-A and B-B is no problem.
> > But for A-B g_rdf determines the intermolecular contribution 
>(which i want) AND
> > the intramolekular contribution (which i wanted to be excluded).
> >
> > Any (nice) ideas to solve this problem for GMX 4.0.7?
> >
> > Long way would be to calculate each intermolecular contribution 
>individual and
> > average over all. Would require some scripting :( so any better 
>solutions are
> > welcome.
> >
> Create a topology with a value of nrexcl sufficient to exclude all
> intramolecular interactions and create a .tpr file from it.  Use 
>that as input
> to g_rdf.
> -Justin
> -------------------------------------------------------------------------------------
> Thanks for the suggestion. But it doesn't really fix the problem (or 
>i don't get it).
> Ok what i have done (as an example only 3 molecules, A1 are all 
>atoms of ring A of molecule 1, other stuff analogous)
> Index group:
> [ A ]
> A1  A2  A3
> [ B ]
> B1  B2  B3
> [ both ]
> A1  B1  A2  B2  A3  B3
> RDF(A-A): chose two times group A
> RDF(B-B): chose two times group B
> RDF(A-B): ?
> If i chose group A and B i get the same result with 'nrexcel 3 or 
>10', i.e. mixing of intra- and intermolecluar A-B distances.
> If i chose 'both' two-times, i get the impression the the result is 
>the RDF between the whole disaccharides, i.e. A1 and B1 are 
>recognised as one molecule (AB)1 and i get the RDF between:
> (AB)1 - (AB)2 ; (AB)1-(AB)3 ; (AB)2-(AB)3
> I tested this also with an index-file with only 1 molecule.
> RDF(A-B) gives the intramolecular RDF
> RDF(both) is zero, because the is only one molecule, center of mass 
>distance must be zero.
> This also doesn't depend on using 'nrexcel 3 or 10'
> Did i made a mistake? Or any further ideas?
> Greetings
> Thomas
> -- 
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