[gmx-users] discrepancy between ED motions and the MD motion
R.S.K.Vijayan
biovijayan at gmail.com
Wed Dec 21 17:39:26 CET 2011
Thanks Tsjerk
Can you plz tell me How do we really conclude that an biologically
relevant motion or a simple relaxation
( i have followed this approach, i also carried out a elastic netwok
modelling based PCA and comapred the lowest mode obtained from EN-NMA with
my PC1- Is this a right approach??)
Thanks
Regards
Vijayan.R
On Wed, Dec 21, 2011 at 10:51 AM, Tsjerk Wassenaar <tsjerkw at gmail.com>wrote:
> Hi Vijayan R.,
>
> Eigenvectors are specific up to a sign. So it's not said the start will
> end up as the negative extreme. It seems your interpolation just shows what
> happens in reverse.
> As a sidenote, do check whether it is a biologically relevant motion, or
> merely relaxation.
>
> Cheers,
>
> Tsjerk
>
> On Dec 21, 2011 4:24 PM, "R.S.K.Vijayan" <biovijayan at gmail.com> wrote:
>
>
> 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>
>>>>
>>>> ==============================**==========
>>>>
>>>> --
>>>> gmx-users mailing list gmx-users at gromacs.org
>>>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
>>>> Please search the archive at http://www.gromacs.org/**
>>>> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
>>>> Please don't post (un)subscribe requests to the list. Use the www
>>>> interface or send it to gmx-users-request at gromacs.org.
>>>> Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>>>>
>>>
>>>
>>>
>>> --
>>> David Mobley
>>> dmobley at gmail.com
>>> 504-383-3662
>>>
>>>
>>>
>>> --
>>> gmx-users mailing list gmx-users at gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>> Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-request at gromacs.org.
>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>
>>
>>
>> --
>> -----------------------
>> *Regards,*
>> Bipin Singh
>>
>>
>> --
>> gmx-users mailing list gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20111221/6dcb9856/attachment.html>
More information about the gromacs.org_gmx-users
mailing list