From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Wed Nov 26 2014 - 05:04:20 CST
> -----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 11:05
> An: Norman Geist; namd-l_at_ks.uiuc.edu
> Betreff: Re: namd-l: anisotropic pressure control
>
> 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?
>
No. Fluctuation == changing box size in Z == NPT == Pressure
If fluctuation only happen in Z this means the pressure target is also only applied to Z.
> 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...
As already meantioned, when using useconstantarea:
Langevinpistontarget == Pzz
The parameter langevinpiston target is also scriptable so what you would want is something like:
Useflexiblecell yes
Useconstantarea yes
set Pstart 1
set Pend = 100
set Pstep = 1
for {set P 0} {$P < $Pend} {incr P $Pstep} {
langevinpistontarget $P
run 1000000
}
>
> 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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