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

[Nilesh Dhumal]

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.
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.
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
>
>
> ========================================
> --
> gmx-users mailing list    gmx-users at gromacs.org
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