From: Maxim Igaev (maxim.igaev_at_Biologie.Uni-Osnabrueck.DE)
Date: Wed Nov 26 2014 - 03:47:41 CST
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?
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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