From: Maxim Igaev (maxim.igaev_at_Biologie.Uni-Osnabrueck.DE)
Date: Wed Nov 26 2014 - 04:04:49 CST
yes, this is what I want, but as far as I know setting UseConstantArea
to yes will allow only fluctuations along the z-axis. This means that I
cannot tell NAMD: "ok, set Pzz to 10 bar" but rather just say "don't
control Pzz in the z-direction, let it fluctuate as it wants to". Or am
I wrong?
In the papers that I read on anisotropic pressure control, it's
explicitly said that the Pzz(target), the Langevin piston target for
Pzz, is linearly increased/decreased. So I've been wondering, where is
this Pzz(target) in the NAMD config...
Regards,
Maxim
> Ah, ok. So you want to apply the pressure in Z only?
> That's possible by:
>
> Useflexiblecell yes
> Useconstantarea yes
>
> This will apply pressure only in Z direction and leave XY untouched.
> Is that what you want?
>
> Norman Geist.
>
>
> > -----Ursprüngliche Nachricht-----
> > Von: Maxim Igaev [mailto:maxim.igaev_at_Biologie.Uni-Osnabrueck.DE]
> > Gesendet: Mittwoch, 26. November 2014 10:46
> > An: Norman Geist
> > Betreff: Re: namd-l: anisotropic pressure control
> >
> > Hi Norman,
> >
> > thanks for your answer. I have a system (a microtubule) that is
> > effectively "infinite" in the z-dimention (via periodical boundary
> > conditions). The system has been equilibrated in the NpT ensemble
> > for several nanoseconds. Pxx, Pyy and Pzz of the pressure tensor
> > are nearly equal, which means the system is not under pressure.
> > What I'd like to do
> > now is to compress/stretch it in the z-dimension by manually
> > increasing/decreasing the Pzz component of the pressure tensor. I
> > know that this is possible since there have been publications about
> > it, in which NAMD was used, but I don't find how it's technically
> > done.
> >
> > langevinPistonTarget option specifies the total target
> > pressure, but not Pxx or Pxy, etc.
> >
> > So my questions is how can I independently control the components of
> > the
> > pressure tensor in the config file? In other words, is there
> > something like Langevin piston target for Pzz?
> >
> > Regards,
> > Maxim
> >
> > Am Wed, 26 Nov 2014 10:22:31 +0100
> > schrieb Norman Geist <norman.geist_at_uni-greifswald.de>:
> >
> > > If you wan't to perform NPT in all dimensions independently use:
> > >
> > > Useflexiblecell yes
> > > Useconstantarea no
> > > Useconstantratio no
> > >
> > > Otherwise please explain what you want to do, most people don't
> > > have time to follow any links and read whole papers.
> > >
> > > Norman Geist.
> > >
> > >
> > > > -----Ursprüngliche Nachricht-----
> > > > Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu]
> > > > Im Auftrag von Maxim Igaev
> > > > Gesendet: Mittwoch, 26. November 2014 09:49
> > > > An: namd-l_at_ks.uiuc.edu
> > > > Betreff: namd-l: anisotropic pressure control
> > > >
> > > > Dear NAMD users,
> > > >
> > > > I'd like to perform anisotropic pressure control simulations to
> > > > stretch/compress my system using the protocol published by Luan
> > > > and Aksimentiev (Phys. Rev. Lett., 2008). Although I understand
> > > > the theory behind it (Martyna et al., 1994), I haven't found any
> > > > information on how to do this technically in the NAMD config
> > > > file. Am I overlooking something? The standard Nose-Hoover
> > > > Langevin piston pressure control allows one to only control the
> > > > total pressure, but not single components of the pressure
> > > > tensor.
> > > >
> > > > I would appreciate any help!
> > > >
> > > > Regards,
> > > > Maxim
> > > >
> > > > ____________________________
> > > >
> > > > Maxim Igaev, M.Sc.
> > > >
> > > > Department of Neurobiology
> > > >
> > > > University of Osnabrueck
> > > >
> > > > http://www.neurobiologie.uni-osnabrueck.de/
> > >
>
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