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" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org>
To: "Discussion list for GROMACS users" <gmx-users@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 <[EMAIL PROTECTED]> 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
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