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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Received on Fri Aug 06 2010 - 19:00:02 PDT
