Dear All:
I did some umbrella sampling and got series of .pdo files. I
want to calculate potential of mean force (PMF) by g_wham command.
However I encount some problems:
when I input the following command:
g_wham pull.pdo -o xx.xvg -hist xx2.xvg
-temp 300
the programme give me the following errors:
:-) G R O M A C S (-:
Giving Russians Opium May Alter Current Situation
:-) VERSION 3.3.3 (-:
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.
:-) g_wham (-:
Option Filename Type Description
------------------------------------------------------------
-o xx.xvg Output xvgr/xmgr file
-hist xx2.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 300 Temperature
-[no]flip bool no Combine halves of profile
-tol real 0.01 Tolerance
Opening file pull.pdo.
gunzip: stdin: not in gzip format
-------------------------------------------------------
Program g_wham, VERSION 3.3.3
Source code file: gmx_wham.c, line: 89
Fatal error:
This does not appear to be a valid pdo file
-------------------------------------------------------
Since it remained me that pull.pdo is not in gzip format, i compress
the fill by gzip command of linux system, and got pull.pdo.gz file,
then i input
g_wham pull.pdo.gz -o xx.xvg -hist
xx2.xvg -temp 300
it still give me the following errors:
:-) G R O M A C S (-:
Good gRace! Old Maple Actually Chews Slate
:-) VERSION 3.3.3 (-:
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.
:-) g_wham (-:
Option Filename Type Description
------------------------------------------------------------
-o xx.xvg Output xvgr/xmgr file
-hist xx2.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 300 Temperature
-[no]flip bool no Combine halves of profile
-tol real 0.01 Tolerance
Opening file pull.pdo.gz.
-------------------------------------------------------
Program g_wham, VERSION 3.3.3
Source code file: gmx_wham.c, line: 89
Fatal error:
This does not appear to be a valid pdo file
-------------------------------------------------------
Since it remaind me that, "This does not appear to be a valid pdo
file", so does my .pdo file has some errors?
I past the head of the .pdo file in the following:
# UMBRELLA 3.0
# Component selection: 1 1 1
# nSkip 1
# Ref. Group ''
# Nr. of pull groups 1
# Group 1 'RIM' Umb. Pos. 3.248000 4.042000 6.703000 Umb. Cons.
4500.000000 4500.000000 4500.000000
#####
0.000000 -0.008039 0.030365 0.047038
0.002000 -0.007788 0.030589 0.046546
0.004000 -0.008109 0.030091 0.044898
0.006000 -0.008317 0.029740 0.043540
0.008000 -0.008357 0.029604 0.042659
0.010000 -0.008538 0.029289 0.041361
0.012000 -0.008690 0.029013 0.040120
0.014000 -0.008694 0.028929 0.039281
0.016000 -0.008703 0.028839 0.038380
.........................................
Does anyone can give me some advise on how to use g_wham command?
any help is appreciate, thank you in advance.
R-X Gu
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