Hello,<br><br><div class="gmail_quote">2012/5/3 Dommert Florian <span dir="ltr"><<a href="mailto:dommert@icp.uni-stuttgart.de" target="_blank">dommert@icp.uni-stuttgart.de</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
On Thu, 2012-05-03 at 07:32 +0200, Albert wrote:<br>
> hello:<br>
><br>
> I wondering are the three thermostat methods: Langevin, Berendsen<br>
> and Nose-Hoover chain are all compatible with semi-isotropy coupling<br>
> style? If I would like to use semi-isotropy coupling method, which one<br>
> would be better?<br>
><br>
> thank you very much<br>
><br>
<br>
Hi,<br>
<br>
what should be coupled in a semi-isotropic manner ? I assume the<br>
pressure and now the question is, which thermostat to apply, isn't it?<br>
<br>
The three mentioned barostats are all of different kinds. While Langevin<br>
provides a thermostating method for implicit solvent, the other<br>
mentioned Thermostats are based on an explicit atom description of the<br>
system. However, the Berendsen thermostat quite old and not symplectic,<br></blockquote><div><br></div><div><br></div><div>I remark that Langevin method is used also for explicit water system! </div><div><br></div><div><br>
</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
which means that the phase space volume is not conserved. Fortunately,<br>
an updated method, the v-rescale thermostat of Bussi et al, has been<br>
published some years ago. It is quite similar to the Berendsen<br>
thermostat, but symplectic and suitable for production and<br>
equilibration. Finally the Nose-Hoover chain (NHC) is based on a<br>
extended Lagrangian for the system you want to simulate and<br>
corresponding equations of motions are applied in order to keep the<br>
temperature constant. NHC is symplectic, too, but not suitable for<br>
equilibration. However, as the only reasonable method for anisotropic<br>
pressure coupling is the Parrinello-Rahman (PR) barostat, or its<br>
extended version MTTK, which relies on the same idea as NHC, I would<br>
assume, that for production a combination of NHC and MTTK is a good<br>
choice. For the equilibration I would use a v-rescale thermostat and the<br>
Berendsen barostat, because PR and MTTK would take far too much time to<br>
achieve equilibrium.<br>
<br>
Hence, it much depends on the purpose, which combination of thermo- and<br>
barostat is the most suitable one.<br>
<br>
/Flo<br>
<br></blockquote><div><br></div><div>Anyway, I think that there is no strict coupling between temperature and pressure coupling:</div><div>You need to keep the tempaerature fixed around a value and the same for pressure, so</div>
<div>I guess any combination v-rescale, NHC, Langevin versus PR or MTTK is, in priciple, right.</div><div><br></div><div>Maybe convergence speed changes, but in this case banchmark are quite useful very welcolme!</div><div>
<br></div><div>best,</div><div>Francesco</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
<br>
> best<br>
> Albert<br>
> --<br>
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<br>
--<br>
Florian Dommert<br>
Dipl. - Phys.<br>
<br>
Institute for Computational Physics<br>
University Stuttgart<br>
<br>
Pfaffenwaldring 27<br>
70569 Stuttgart<br>
<br>
EMail: <a href="mailto:dommert@icp.uni-stuttgart.de">dommert@icp.uni-stuttgart.de</a><br>
Homepage: <a href="http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert" target="_blank">http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert</a><br>
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Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br></blockquote></div><br><br clear="all"><div><br></div>-- <br>Cordiali saluti, Dr.Oteri Francesco<br>