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

[Justin A. Lemkul]

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_Sampling

-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

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