[gmx-users] g_wham -sym

[Jochen Hub]

Hi,

I think g_wham cannot symmetrize around a non-zero point. You'll have to
write a little awk script or so and this yourself. Or edit the g_wham code.

-zprof0 is not what you need. It sets the PMF to zero at a reference
point, where the free energy is defined to zero.

Best,
Jochen


Am 8/10/13 8:59 AM, schrieb Shima Arasteh:
> Thanks,
> I defined a new 0.0 position by  -zprof0, and shifted the profile energy to a new 0.0.
> 
> # g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kca -zprof0 -1.081898 -sym
> 
> But -sym gets me an error:
> 
> Fatal error:
> 
> Cannot symmetrize profile around z=0 with min=-1.312664 and max=-1.081898
> 
> 
> Why does the g_wham tries to still symmetrize the profile around z=0?
> Would you please give me any suggestion?
> 
>  
> Sincerely,
> Shima
> 
> 
> ----- Original Message -----
> From: Justin Lemkul <jalemkul at vt.edu>
> To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
> Cc: 
> Sent: Friday, August 9, 2013 2:40 PM
> Subject: Re: [gmx-users] g_wham -sym
> 
> 
> 
> On 8/9/13 5:48 AM, Shima Arasteh wrote:
>> Hi,
>>
>> I use the
>> g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kca -sym
>>
>>
>> I' d like to know if it is possible to symmetrize the profile around a non-zero point? forexample z=60?
>>
> 
> Use -zprof0.
> 
> -Justin
> 

-- 
---------------------------------------------------
Dr. Jochen Hub
Computational Molecular Biophysics Group
Institute for Microbiology and Genetics
Georg-August-University of Göttingen
Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
Phone: +49-551-39-14189
http://cmb.bio.uni-goettingen.de/
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