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Re: [ESPResSo-users] how to run NPT simulation
From: |
Axel Arnold |
Subject: |
Re: [ESPResSo-users] how to run NPT simulation |
Date: |
Fri, 11 Feb 2011 16:46:49 +0100 |
User-agent: |
KMail/1.13.5 (Linux/2.6.34.7-0.7-desktop; KDE/4.4.4; x86_64; ; ) |
On Friday 11 February 2011 09:24:47 Ulf Schiller wrote:
> Yonglei Wang wrote:
> > Hej
> >
> > I noticed that we can simulate NPT ensemble with this package but I
> > checked all scripts and found there is only one npt.tcl file which is
> > used to validate this package during installation. So I want to know how
> > can I implement the NPT simulation in detail? I mean, if we generate all
> > particle coordinates with very low number density, then run the NPT
> > simulation to shrink the simulation box. How should I do fulfill this
> > simulation?
>
> Yonglei,
>
> the following reference describes the NPT algorithm in more detail:
>
> J. Chem. Phys. 111, 4453 (1999); doi:10.1063/1.479208
>
> Note in particular the discussion on oscillating behavior. I believe
> there is no general recipe how to setup an NPT simulation. You will have
> to tune the parameters for your specific system.
Hi,
since we are often interested in NVT simulations, we use normally other tricks
to setup our systems, which I guess will also be faster when using NPT.
Starting from a rather large box, it might take rather long for NPT to
equilibrate to the correct box size, therefore, starting at higher densities
might be faster.
To start a high densities reliably, the short ranged interactions can be
capped, that is, their singularity is replaced by a low barrier, which
gradually can be risen. This barrier is set by inter ljforcecap for the
Lennard-Jones potential. See for example the script samples/lj_liquid.tcl.
Regards,
Axel
--
JP Dr. Axel Arnold
ICP, Universität Stuttgart
Pfaffenwaldring 27
70569 Stuttgart, Germany
Email: address@hidden
Tel: +49 711 685 67609