[gmx-users] Free energy tutorial 6

[Justin A. Lemkul]

murat özçelik wrote:
> hi! again..
> ı  collect all .xvg files into a single file.. and run g_bar
> 

You can't do that. g_bar requires multiple input files, as I stated before.

-Justin

> g_bar -f md.xvg -o -oi -oh
> 
> the program gave me below result
> 
> hayalet at ubuntu:~/Masaüstü$ g_bar -f md.xvg -o -oi -oh
>                          :-)  G  R  O  M  A  C  S  (-:
> 
>                  Good ROcking Metal Altar for Chronical Sinners
> 
>                             :-)  VERSION 4.5.5  (-:
> 
>         Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
>    &nbs! p ;  Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton 
> Feenstra,
>         Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
>            Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
>                 Michael Shirts, Alfons Sijbers, Peter Tieleman,
> 
>                Berk Hess, David van der Spoel, and Erik Lindahl.
> 
>        Copyright (c) 1991-2000, University of Groningen, The Netherlands.
>             Copyright (c) 2001-2010, The GROMACS development team at
>         Uppsala University & The Royal Institute of Technology, Sweden.
>       &nbs! p;      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.
> 
>                                 :-)  g_bar  (-:
> 
> Option     Filename  Type         Description
> ------------------------------------------------------------
>   -f &nbs! p;& nbsp;      md.xvg  Input, Opt!, Mult. xvgr/xmgr file
>   -g       ener.edr  Input, Opt., Mult. Energy file
>   -o        bar.xvg  Output, Opt! xvgr/xmgr file
>  -oi     barint.xvg  Output, Opt! xvgr/xmgr file
>  -oh  histogram.xvg  Output, Opt! xvgr/xmgr file
> 
> Option       Type   Value   Description
> ------------------------------------------------------
> -[no]h       bool   no      Print help info and quit
> -[no]version bool   no      Print version info and quit
> -nice        int    0       Set the nicelevel
> -[no]w       bool   no! & nbsp;     View output .xvg, .xpm, .eps and 
> .pdb files
> -xvg         enum   xmgrace  xvg plot formatting: xmgrace, xmgr or none
> -b           real   0       Begin time for BAR
> -e           real   -1      End time for BAR
> -temp        real   -1      Temperature (K)
> -prec        int    2       The number of digits after the decimal point
> -nbmin       int    5       Minimum number of blocks for error estimation
> -nbmax       int    5  &nbs! p;     Maximum number of blocks for error 
> estimation
> -nbin        int    100     Number of bins for histogram output
> 
> md.xvg: 0.0 - 5000.0; lambda = 1.000
>     foreign lambdas: 0.000 (5250021 pts) 0.050 (5250021 pts)
> 
> 
> Writing histogram to histogram.xvg
> 
> Back Off! I just backed up histogram.xvg to ./#histogram.xvg.1#
> 
> No results to calculate.
> hayalet at ubuntu:~/Masaüstü$
> 
> Where I am doing wrong
> 
> please help me .. thanks..
> 
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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