[gmx-users] g_wham problem

[Guillem Portella]

Hi Arnab,

First of all I would strongly suggest you to check the mailing list archieves 
before posting. You'll see that the g_wham code is broken. There exist a 
fixed version from Dr. Bostick, but it's not included in the package.
If you want, you can ask him for his working version, which I used 
succesfully. 

The argument parsing in the standard version is wrong, there's no way it can 
work. You can also try to fix it yourself.

Regards,

Guillem


On Friday 30 September 2005 16:57, arnab mukherjee wrote:
> Dear Users,
> I have encountered a problem with g_wham and I will appreciate any help
> regarding this.
>
> I tried to do umbrella sampling using pull code. I have got pull.pdo file.
> then when I type the command
> g_wham pull.pdo
>
> i get an error saying that my .pdo file is not a .pdo file? I checked the
> source code. there is a
> mismatch between the word UMBRELLA and Buffer1 which reads from .pdo file
> and Buffer1 should
> be UMBRELLA too. Can anybody pls. tell me how to use the g_wham if I am
> giving the wrong command.
>
>
> The intial few lines of my pull.pdo file
>
> # UMBRELLA 3.0
> # Component selection: 1 1 1
> # nSkip 10
> # Ref. Group 'DNA'
> # Nr. of pull groups 1
> # Group 1 'DM1' Umb. Pos. -0.312000 -0.949000 0.051000 Umb. Cons.
> 1000.000000 1000.000000 1000.000000
> #####
> 0.000000 0.271045 0.818249 -0.784236
> 0.020000 0.271507 0.817984 -0.783464
> 0.040000 0.272017 0.817565 -0.782536
> 0.060000 0.272681 0.817110 -0.781317
> 0.080000 0.273403 0.816726 -0.779726
> 0.100000 0.274028 0.816400 -0.777928
> 0.120000 0.274420 0.816246 -0.776361
> 0.140000 0.274662 0.816204 -0.775056
> .....
> ......
> g_wham pull.pdo
> The error is (after the gromacs user commands)
>
> Opening file pull.pdo.
>
> gunzip: stdin: not in gzip format
> -------------------------------------------------------
> Program g_wham, VERSION 3.3_beta_20050202
> Source code file: gmx_wham.c, line: 90
>
> Fatal error:
> This does not appear to be a valid pdo file
>
> Thanking in anticipation of your reply,
>
>
> with best regards
>
>
> --
> Arnab Mukherjee
> post doctorate
> Chimie
> Ecole Normale Superieure

-- 
***************************************************************
 Guillem Portella 
 Computational biomolecular dynamics group at the 
 Max Planck Institute for Biophysical Chemistry 
 Am Fassberg 11 
 D-37077 Goettingen -- Germany --
 phone: ++49-551-2012309 
 fax: ++49-551-2012302 
 Email: gportel at gwdg.de 
 webpage: www.mpibpc.mpg.de/abteilungen/073/gportel/index.html
***************************************************************