[gmx-users] g_wham and PMF problem
Sudha Mani Karra
karra.md at gmail.com
Tue Jul 3 18:46:06 CEST 2007
Hi..
I listed all the zipped files separately as you said.
g_wham -bins 1000 pull1.pdo.gz pull2.pdo.gz pull3.pdo.gz pull4.pdo.gz
pull5.pdo.gz -temp 298 -o pmf.xvg
I still have the same problem.
:-) G R O M A C S (-:
GRoups of Organic Molecules in ACtion for Science
:-) VERSION 3.3.1 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2006, 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.
:-) g_wham (-:
Option Filename Type Description
------------------------------------------------------------
-o pmf.xvg Output xvgr/xmgr file
-hist histo.xvg Output xvgr/xmgr file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-nice int 0 Set the nicelevel
-[no]w bool no View output xvg, xpm, eps and pdb files
-[no]xvgr bool yes Add specific codes (legends etc.) in the output
xvg files for the xmgrace program
-min real 0 Minimum coordinate in profile
-max real 0 Maximum coordinate in profile
-bins int 1000 Number of bins in profile
-[no]prof bool yes Only calculate min and max
-temp real 298 Temperature
-[no]flip bool no Combine halves of profile
-tol real 0.01 Tolerance
Opening file pull1.pdo.gz.
-------------------------------------------------------
Program g_wham, VERSION 3.3.1
Source code file: gmx_wham.c, line: 90
Fatal error:
This does not appear to be a valid pdo file
-------------------------------------------------------
That is the error which I get....
Thank You for your input..
Also if it is not bothering you can you please send me the modified version
of g_wham by David Bostick else I shall check it once again as I couldn't
find it earlier.
Thanks,
SK
On 7/3/07, Lu Lanyuan <lulanyuan at msn.com> wrote:
>
> I just zipped alll the *.pdo files seperately and listed them all when
> using g_wham. It's like g_wham <options> pull1.pdo.gz pull2.pdo.gz ... In
> the old gromacs versions like 3.1.4, the g_wham was broken and I was using
> a version modifined by David Bostick. You can search the mailing list for
> that information. I'm not sure whether the old problem of g_wham was fixed
> in 3.3.1.
> Lanyuan Lu
>
>
> >From: "Sudha Mani Karra" <karra.md at gmail.com>
> >Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> >To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> >Subject: Re: [gmx-users] g_wham and PMF problem
> >Date: Tue, 3 Jul 2007 10:08:33 -0500
> >
> >Hi Mark,
> > when I give only one file in the input for g_wham,
> >
> >g_wham -o pmf.xvg -hist pull1.pdo ,
> >
> >It asks me to give a series of inputs.The error which I get is
> > :-) g_wham (-:
> >
> >Option Filename Type Description
> >------------------------------------------------------------
> > -o pmf.xvg Output xvgr/xmgr file
> >-hist pull1.pdo.xvg Output xvgr/xmgr file
> >
> > Option Type Value Description
> >------------------------------------------------------
> > -[no]h bool no Print help info and quit
> > -nice int 0 Set the nicelevel
> > -[no]w bool no View output xvg, xpm, eps and pdb files
> > -[no]xvgr bool yes Add specific codes (legends etc.) in the
> >output
> > xvg files for the xmgrace program
> > -min real 0 Minimum coordinate in profile
> > -max real 0 Maximum coordinate in profile
> > -bins int 100 Number of bins in profile
> > -[no]prof bool yes Only calculate min and max
> > -temp real 298 Temperature
> > -[no]flip bool no Combine halves of profile
> > -tol real 0.01 Tolerance
> >
> >-------------------------------------------------------
> >Program g_wham, VERSION 3.3.1
> >Source code file: gmx_wham.c, line: 314
> >
> >Fatal error:
> >You need to specify a series of pdo files as input
> >---------------------------------------------------
> >
> >Appreciate your help.Thanks,
> >SK
> >
> >
> >
> >
> >
> >
> >
> >On 7/3/07, Mark Abraham <mark.abraham at anu.edu.au> wrote:
> >>
> >> > Hey Mark,
> >> > Appreciate your immediate response.You can find the
> >>input and
> >> > the
> >> > error below:
> >> > g_wham -o pmf.xvg -hist pull1.pdo pull2.pdo pull3.pdo pull4.pdo
> >>pull5.pdo
> >>
> >>g_wham -h suggests that -hist won't accept multiple input files.
> >>Only a
> >>few GROMACS utilities will do magic concatenation for you. Have a
> >>look at
> >>the file format and see what you need to do with a text editor or
> >>command
> >>line tools.
> >>
> >> > Opening file pull2.pdo.
> >> >
> >> > gunzip: stdin: not in gzip format
> >> > -------------------------------------------------------
> >> > Program g_wham, VERSION 3.3.1
> >> > Source code file: gmx_wham.c, line: 90
> >> >
> >> > Fatal error:
> >> > This does not appear to be a valid pdo file
> >> > -------------------------------------------------------
> >>
> >>Does g_wham -o pmf.xvg -hist pull1.pdo work?
> >>
> >>Mark
> >>
> >>_______________________________________________
> >>gmx-users mailing list gmx-users at gromacs.org
> >>http://www.gromacs.org/mailman/listinfo/gmx-users
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> >>
>
>
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