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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>>> (20100803) __________
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>>> Tuto zpravu proveril ESET NOD32 Antivirus.
>>>
>>> http://www.eset.cz
>>>
>>
>>
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Received on Mon Jun 20 2011 - 12:30:03 PDT
