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

[Nilesh Dhumal]

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