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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>
>
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Received on Mon Jun 20 2011 - 10:30:03 PDT
