[gmx-users] -ve value of z in g_wham

[Justin A. Lemkul]

Nilesh Dhumal wrote:
> If I am geting -ve value if z in g_wham then zero is my initial distance
> or reference distance.

That means your pull group has a coordinate that is negative with respect to the 
reference group at some point during (at least) one of the umbrella sampling 
windows.  Zero, in this case, corresponds to an equivalent coordinate in the 
pull dimension.

Without a substantially more detailed description of your system and what you've 
done, you're unlikely to get anything more helpful.

-Justin

> Nilesh
> 
> 
> On Sat, December 11, 2010 9:43 pm, Justin A. Lemkul wrote:
> 
>> Nilesh Dhumal wrote:
>>
>>> Hello,
>>> I trying to run umbrella sampling simulation for system.
>>>
>>>
>>> After running g_wham command I am geting some negative value of z along
>>> x axis.
>>>
>>> g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kcal
>>>
>>> Can any one tell why I am geting -ve value or what is the significance
>>> of this.
>>>
>> That means the coordinate of your pull group is less than that of your
>> reference group along the reaction coordinate.  The reason for that
>> depends on how you constructed your pull and reference groups and how you
>> carried out the umbrella sampling.
>>
>> -Justin
>>
>>
>>> Nilesh
>>>
>>>
>>>
>>>
>>>
>> --
>> ========================================
>>
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>
>> ========================================
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> 
> 
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================