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
others.
Copyright (c) 1991-2000, University of Groningen, The
Netherlands.
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
and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version
2
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
cpt
-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
(ps)
-------------------------------------------------------
Program ngmx, VERSION 4.0.7
Source code file: ../../../../src/gmxlib/gmxfio.c, line: 737
Can not open file:
topol.tpr
-------------------------------------------------------
"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 <[email protected]> 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-B
>
> 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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