[gmx-users] about g_wham

[Jochen Hub]

Hi,

sorry for the late answer. But there is a completely new g_wham in the
most recent gmx version 4.xx. With this one, the error

"This does not appear to be a valid pdo file"

does not occur any more. And the new g_wham provides a lot of new
featues, too.

Best,
Jochen



anirban polley wrote:
> Hi all,
>           Could you please tell me why g_wham does not give the correct
> result? After doing umbrella sampling with mdrun, I got the .pdo file which
> is like
> 
> # UMBRELLA      3.0
> # Component selection: 0 0 1
> # nSkip 1
> # Ref. Group 'DPP'
> # Nr. of pull groups 1
> # Group 1 'PIP'  Umb. Pos. 3.388542  Umb. Cons. 100.000000
> #####
> 0.000000        1.650988
> 0.002000        1.650989
> 0.004000        1.651020
> 0.006000        1.651055
> 0.008000        1.651139 .........
> 
>               Now, when I try to analysis it by g_wham, I have stuck. Could
> you please tell me the right method?
> 1. g_wham -max 1.7779 -min .8988 -temp 310 -o  pull_pip2_dppc.pdo.
> The error message is:
> -------------------------------------------------------
> Program g_wham, VERSION 3.3.3
> Source code file: gmx_wham.c, line: 313
> 
> Fatal error:
> You need to specify a series of pdo files as input
> -------------------------------------------------------
> Question: How can I get the series of pdo file? Did it mean that I have to
> vary the Umb. const. and run it many times and get many .pdo files?
> 
> 
> 2.       g_wham pull_pip2_dppc.pdo -max 1.7779 -min .8988 -temp 310 -o -hist
>  The error is :
> 
> Opening file pull_pip2_dppc.pdo.
> 
> gzip: 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
> -------------------------------------------------------
> 
> 3. Now, I tried it by converting .gz file as an input
> 
>  g_wham pull_pip2_dppc.pdo.gz -max 1.7779 -min .8988 -temp 310 -o
> 
> The error is:
> Opening file pull_pip2_dppc.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
> -------------------------------------------------------
> 
> 
> Could you please tell me why it gives error again and again? What is the
> wrong that I have done? How Can I get the correct answer?
> 
> Please, tell me the answer? I am eagerly waiting for your advise.
> Regards,
> Anirban
> 
> 
> 
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-- 
************************************************
Dr. Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
Tel.: +49 (0)551 201-2312
************************************************