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

[Justin A. Lemkul]

Nilesh Dhumal wrote:
> My box size is 4.5 4.5 4.5 (in nm)90 90 90
> 

Seems awfully large for only 128 waters.  I just wonder if the box is distorting 
during the simulation such that the periodic distance becomes the reference 
distance, hence the switch between positive and negative distances.  This 
concept is discussed in the tutorial I linked before.

> My boss want to see the natue of plot before going for sampling.

You can't generate a PMF curve from a single simulation.  Any resulting plot 
will be completely useless.  Please reference the literature about the method, 
as well as the simple explanation I provide in the tutorial.

-Justin

> Nilesh
> 
> On Wed, December 29, 2010 1:04 pm, Justin A. Lemkul wrote:
> 
>> Nilesh Dhumal wrote:
>>
>>> I have a system with 128 water molecules and a ion pair of ionic
>>> liquids i.e. one cation and one anion. the reaction corrdination is the
>>> distance between cation and anion. Initial distance between cation-anion
>>> is 0.8 nm.
>> What is the size of the smallest box vector?
>>
>>
>>> I have pasted some part of md file
>>>
>>>
>>> ; Pull code
>>> pull            = umbrella pull_geometry   = distance pull_dim        = Y
>>> Y Y
>>> pull_start      = NO             ; define initial COM distance > 0
>>> ;reftype   = com
>>> pull_ngroups    = 1 pull_group0     = EMI pull_group1     = ETS pull_init1
>>> = 0.0
>>> pull_rate1      = 0.01          ; 0.01 nm per ps = 10 nm per ns pull_k1
>>> = 1000          ; kJ mol^-1 nm^-2
>>>
>>>
>>>
>>> I run the simulation for 2ns then I run g_wham.
>>>
>> You're only running one simulation?  That's not appropriate for umbrella
>> sampling.
>>
>> http://www.gromacs.org/Documentation/Tutorials#Pull_Code_and_Umbrella_Sam
>> pling
>>
>> -Justin
>>
>>
>>> I more interested in structure where caion and anion are close ~0.4 nm.
>>>
>>>
>>> After ploting PMF I found that I have -ve value of z.
>>>
>>>
>>> NIlesh
>>>
>>>
>>> On Wed, December 29, 2010 12:51 pm, Justin A. Lemkul wrote:
>>>
>>>
>>>> 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
>>>>
>>>>
>>>>
>>>> ========================================
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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
>>
>>
>> ========================================
>>
>>
>>
> 
> 
> 

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

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

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