[gmx-users] discrepancy between ED motions and the MD motion

[R.S.K.Vijayan]

Hi all

I carried out a distance analysis between two domains with respect to time
based on the center of mass. Subsequently i also carried out a PCA based
essential dynamics to identify the global/biologically relevant motions.
The strange and inconsistent  result i find here is

when i calculate the distance using the MD (progressive fitted) trajectory,
I find that the two domains of interest move apart with respect to time.

on the contrary a  ED followed by a smoothed interpolation between the two
extreme motions revelas that the two domains move closer to each other in a
concerted fashion.

does any one has an explanation for this discrepancy between ED motions and
the MD motion ???

Thanking you in advance

Regards
Vijayan.R



On Tue, Dec 20, 2011 at 2:28 AM, bipin singh <bipinelmat at gmail.com> wrote:

> Thanks a lot for your suggestions.
>
> On Mon, Dec 19, 2011 at 21:00, David Mobley <dmobley at gmail.com> wrote:
>
>> Yes, changing the net charge of the system is something that is rather
>> complicated in fact (one can plunge ahead and do it while ignoring the
>> complications, but the results will typically be rather system-size
>> dependent and essentially wrong). For more details refer to the Kastenholz
>> and Hunenberger papers from J. Chem. Phys (2006 or 2007) and references
>> therein. The good news is that for simple spherical ions K&H have worked
>> out the relevant corrections. The bad news is that if you move away from
>> simple spherical ions you've got problems.
>>
>> David Mobley
>>
>>
>>
>> On Fri, Dec 16, 2011 at 6:41 AM, Justin A. Lemkul <jalemkul at vt.edu>wrote:
>>
>>>
>>>
>>> bipin singh wrote:
>>>
>>>> Hello,
>>>>
>>>> I am willing to study the free energy of binding of a cation (Ca++) to
>>>> the protein and I am following the free energy tutorial
>>>> provided by Justin
>>>> (http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin/**
>>>> gmx-tutorials/free_energy<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy>
>>>> ).
>>>> Please let me know whether the settings for this type of study would
>>>> be same as given in the tutorial for ligand-Protein
>>>> binding free energy calculation or it need some different approach:
>>>>
>>>
>>> By decoupling a Ca2+ ion, you are removing 2 charges from the system.  I
>>> don't know how to properly treat such a case (perhaps someone else can
>>> comment), but likely you'll find such topics in the literature.  A better
>>> approach may be umbrella sampling, but again the literature should point
>>> you to reasonable methodology.  I'm sure others have dealt with such
>>> questions before.
>>>
>>> -Justin
>>>
>>>
>>>  The setting from the ligand-Protein binding free energy calculation
>>>> are given as:
>>>>
>>>>
>>>>  van der Waals coupling:
>>>>
>>>>     sc-alpha          = 0.5     ; use soft-core for LJ (de)coupling
>>>>     sc-sigma          = 0.3
>>>>     sc-power          = 1
>>>>     couple-moltype    = LIG
>>>>     couple-intramol   = no
>>>>     couple-lambda0    = none    ; non-interacting dummy in state A
>>>>     couple-lambda1    = vdw     ; only vdW terms on in state B
>>>>
>>>> Coulombic coupling:
>>>>
>>>>     sc-alpha          = 0       ; soft-core during (dis)charging can
>>>> be unstable!
>>>>     sc-sigma          = 0
>>>>     couple-moltype    = LIG
>>>>     couple-intramol   = no
>>>>     couple-lambda0    = vdw     ; only vdW terms in state A (the
>>>> previous state B is now A)
>>>>     couple-lambda1    = vdw-q   ; all nonbonded interactions are on in
>>>> state B
>>>>
>>>>
>>>>
>>> --
>>> ==============================**==========
>>>
>>> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>>
>>> ==============================**==========
>>>
>>> --
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>>>
>>
>>
>>
>> --
>> David Mobley
>> dmobley at gmail.com
>> 504-383-3662
>>
>>
>>
>> --
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>
>
>
> --
> -----------------------
> *Regards,*
> Bipin Singh
>
>
> --
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