Thank you so much Marek,
I was planning to add a glass layer into my simulations but looks like
it is not going to be as easy as it looks.
best
peker
2011/6/20 Marek Maly <marek.maly.ujep.cz>:
> Hi Peker,
>
> If you are attempting to do such simulations in explicit solvent, I am
> afraid (however I am not sure) that you cant't "get rid of periodic BC's".
>
> Here is my approach, although I am really not sure if is the ideal one ...
>
> #1
> Create "sufficiently big" surface (in my case cca 90 x 90 x 18 A)
>
> Size should be "sufficient" to minimize influence of border-inhomogenities
> as
> you can not create infinite surface in Amber. Thickness should be also
> sufficient
> to not underestimate eventual ligand/surface interaction due to too thin
> surface
> representation.
>
> #2
> Then I placed my ligand to central part of my surface
>
>
>
> #3
> I placed cca 40A above the ligand the same surface with the same
> side towards the ligand as in case of "bottom surface" so in fact
> I simulated ligand inside the slit "sitting" on one of that two surfaces.
>
> I decided to do this to have symmetric conditions from both sides of
> ligand ( to decrease ligand interaction with image of the second side of
> the surface )
> as the thickness of water layer which you can put under your surface (to
> decrease sufficiently interaction with vertical images) with ligand is
> strongly
> limited due to hardware speed limitations. If there is no HW limitations
> you can simply
> add sufficient layer of water above your ligand and that's it ...
>
> But it depends, if your surface (and eventually also your ligand) do not
> contains ions so the association with the ligand is just of "hydrophobic"
> character you can in my opinion put under your ligand just cca 15-20A of
> water as vertical images will almost not
> interfere here with your original system.
>
>
> Any other contributions to this topic are welcomed !
>
> Best,
>
> Marek
>
>
>
>
>
>
>
>
> Dne Mon, 20 Jun 2011 19:17:17 +0200 peker milas <pekermilas.gmail.com>
> napsal/-a:
>
>> Hi Marek,
>>
>> I recently intended to make a similar calculation that you were
>> mentioning in your email. I mean a molecule on a solid surface.
>> Honestly i couldn't figure out where should i start from. Can you give
>> me some ideas about this sort of a system ? I mean like, how can i get
>> rid of periodic BC's ? because if i use them in the simplest way as it
>> described in tutorials, i will be having replicas of molecule
>> everywhere.
>>
>> best
>> peker
>>
>> 2010/8/6 Marek Maly <marek.maly.ujep.cz>:
>>> Dear all it seems that for my problems with surface stabilisation is
>>> responsible
>>>
>>> ibelly incompatibility with Langevin thermostat ( ntt=3 ) which I
>>> usually
>>> prefer.
>>>
>>> With ntt=1 seems crystal stabilisation OK, in another words ibelly
>>> works as
>>>
>>> one suppose it should work.
>>>
>>> Best wishes,
>>>
>>> Marek
>>>
>>>
>>>
>>>
>>> Dne Tue, 03 Aug 2010 20:35:28 +0200 Marek Maly <marek.maly.ujep.cz>
>>> napsal/-a:
>>>
>>>> Dear all,
>>>>
>>>> I am trying to simulate interaction between hydroxyapatite (HA) and
>>>> given
>>>> polyurethane (PU).
>>>>
>>>> I successfully constructed and parametrised my system but I still have
>>>> some particular problems and
>>>>
>>>> I would be very grateful for your advices here.
>>>>
>>>>
>>>> Problem #1
>>>>
>>>> The most important problem is surface stabilisation during NPT
>>>> simulation.
>>>>
>>>> I would like to fix (if possible) all atoms of the surface during
>>>> simulation.
>>>>
>>>> If this is not possible (because of changes of simul. box volume during
>>>> NPT run) I would like
>>>>
>>>> at least prevent the crystal atoms from disordering. It means that
>>>> small
>>>> PROPORTIONAL changes
>>>>
>>>> in distances between surface atoms are not the problem but disordering
>>>> of
>>>> atoms of the surface
>>>>
>>>> indeed problem is because it changes surface structure which in turn
>>>> affects significantly interaction with my polymer.
>>>>
>>>> For my first attempt I used "ibelly = 1" constraint with old definition
>>>> of
>>>> bellymask since I naturally wanted to use
>>>>
>>>> pmemd for production run.
>>>>
>>>> The *.in files (minimisation, heating, density equil., prod. run) are
>>>> attached.
>>>>
>>>> Using this strategy I obtained relatively promising result with the
>>>> polymer nicely condensed on the surface
>>>>
>>>> but unfortunately all the HA surface atoms were during the simulation
>>>> partially disordered. Moreover overall dimensions of the crystal
>>>>
>>>> changed from original cca 45A x 52A x 13A to final cca 75A x 89A x 18A.
>>>>
>>>> This change is illustrated on attached picture Illustrations.png
>>>> (please
>>>> see there Fig. 3 and Fig. 4)
>>>>
>>>> So where is the problem ? Did I some mistake in "*.in" files or is
>>>> belly
>>>> constraint unsuitable here and is better
>>>>
>>>> to use harmonic RESTRAINT with very high "restraint_wt" value ? Or is
>>>> there any other choice ?
>>>>
>>>>
>>>>
>>>> problem #2
>>>>
>>>> For this kind of simulation one would probably prefer simulation box
>>>> where
>>>> the crystal surface is on the bottom side
>>>>
>>>> of the box with lateral sides perpendicular to this surface so the
>>>> water
>>>> is only above the surface (or also under but just very small layer like
>>>> 5A) in perpendicular direction.
>>>>
>>>> I wanted to achieve this by placing 4 molecules of H2O in the upper
>>>> coroners of such "hypothetical box" (please see attached
>>>>
>>>> Illustrations.png ( see there Fig. 1 ) and using 0 A spacing )(in the
>>>> picture I used spacing 5A). But the result after solvation is not
>>>>
>>>> in agreement with my expectation as it is clear from Illustrations.png
>>>> (
>>>> see there Fig. 2 ).
>>>>
>>>> Is there any trick to achieve above desired simul. box orientation
>>>> regarding the crystal surface ?
>>>>
>>>> For example is it possible to define explicitly some of the box
>>>> dimensions
>>>> ?
>>>>
>>>>
>>>>
>>>> problem #3
>>>>
>>>> As I mentioned above I used old style for specifying belly residuies to
>>>> allow constraint calculation in pmemd.
>>>>
>>>> Unfortunately pmemd (in Amber 10) has problem to accept individual H
>>>> atoms. In hydroxyapatite there are H atoms
>>>>
>>>> as the parts of OH groups, but since Materials Studio has his specific
>>>> way/order in writing atoms of crystals into PDB I
>>>>
>>>> decided to use for each type of atom one corresponding residuum
>>>> however I
>>>> parametrised all atoms inside their natural
>>>>
>>>> groups in HA so for example H residuum I parametrised in antechamber
>>>> as a
>>>> part of OH group.
>>>>
>>>> There is no such problem for P,O and Ca atoms just for H so at the end
>>>> I
>>>> have to use sander (here is no such problem)
>>>>
>>>> for the whole simulation. So my question is : Is this pmemed
>>>> restriction
>>>> present also in Amber 11 ?
>>>>
>>>> If yes, why (again in sander there is no such restriction) ?
>>>>
>>>>
>>>>
>>>> Thanks a lot in advance for any advices/comments !
>>>>
>>>>
>>>> Best wishes,
>>>>
>>>> Marek
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
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>>>> Tuto zpravu proveril ESET NOD32 Antivirus.
>>>>
>>>> http://www.eset.cz
>>>>
>>>
>>>
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>
>
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Received on Tue Jun 21 2011 - 05:30:03 PDT
