<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">
<div class="HOEnZb"><div class="h5">On Thu, 2012-05-03 at 10:48 +0200, francesco oteri wrote:<br>
> Hello,<br>
><br>
> 2012/5/3 Dommert Florian <<a href="mailto:dommert@icp.uni-stuttgart.de">dommert@icp.uni-stuttgart.de</a>><br>
> On Thu, 2012-05-03 at 07:32 +0200, Albert wrote:<br>
> > hello:<br>
> ><br>
> > I wondering are the three thermostat methods: Langevin,<br>
> Berendsen<br>
> > and Nose-Hoover chain are all compatible with semi-isotropy<br>
> coupling<br>
> > style? If I would like to use semi-isotropy coupling method,<br>
> 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<br>
> the<br>
> pressure and now the question is, which thermostat to apply,<br>
> isn't it?<br>
><br>
> The three mentioned barostats are all of different kinds.<br>
> While Langevin<br>
> provides a thermostating method for implicit solvent, the<br>
> other<br>
> mentioned Thermostats are based on an explicit atom<br>
> description of the<br>
> system. However, the Berendsen thermostat quite old and not<br>
> symplectic,<br>
><br>
><br>
><br>
><br>
> I remark that Langevin method is used also for explicit water system!<br>
<br>
</div></div>But there a big question arises to me. The thermostatting by Langevin is<br>
achieved due to random kicks. If I simulate all atoms explicitly, there<br>
is only vacuum between the atoms. Where do the random kicks come from<br>
and how do I set gamma, which is actually related to the viscosity of<br>
the medium I am simulating in? If my medium is vacuum, then gamma should<br>
be zero, shouldn't it, and gamma=0 means no coupling, and hence,<br>
Newton's equation of motion are recovered.<br>
<br>
I am not an expert with the Langevin thermostat, so this are serious<br>
questions that arise to me now. Furthermore I also thought, that<br>
Langevin dynamics were exactly established for a description of a system<br>
within a medium.<br>
<br></blockquote><div><br></div><div>Implicit Implicit solvent means accounting for the solvent presence without including water atoms, look at <a href="http://en.wikipedia.org/wiki/Implicit_solvation">http://en.wikipedia.org/wiki/Implicit_solvation</a> for details.</div>
<div><br></div><div>Regarding the collision source, it is water! The gamma value represent the average collision frequence experienced by a protein atoms against water in solution. </div><div>You have no water, so it models the water presence. </div>
<div>In implicit water simulation, usually a value close to 50 ps-1 (the experimental values) is used, while for explicit water is used a value around 2-5ps-1 bacause </div><div>water is present so it actually collides with protein.</div>
<div><br></div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
/Flo<br>
<div class="HOEnZb"><div class="h5"><br>
<br>
><br>
><br>
><br>
><br>
><br>
> which means that the phase space volume is not conserved.<br>
> Fortunately,<br>
> an updated method, the v-rescale thermostat of Bussi et al,<br>
> 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<br>
> a<br>
> extended Lagrangian for the system you want to simulate and<br>
> corresponding equations of motions are applied in order to<br>
> keep the<br>
> temperature constant. NHC is symplectic, too, but not suitable<br>
> for<br>
> equilibration. However, as the only reasonable method for<br>
> anisotropic<br>
> pressure coupling is the Parrinello-Rahman (PR) barostat, or<br>
> its<br>
> extended version MTTK, which relies on the same idea as NHC, I<br>
> would<br>
> assume, that for production a combination of NHC and MTTK is a<br>
> good<br>
> choice. For the equilibration I would use a v-rescale<br>
> thermostat and the<br>
> Berendsen barostat, because PR and MTTK would take far too<br>
> much time to<br>
> achieve equilibrium.<br>
><br>
> Hence, it much depends on the purpose, which combination of<br>
> thermo- and<br>
> barostat is the most suitable one.<br>
><br>
> /Flo<br>
><br>
><br>
><br>
> Anyway, I think that there is no strict coupling between temperature<br>
> and pressure coupling:<br>
> You need to keep the tempaerature fixed around a value and the same<br>
> for pressure, so<br>
> I guess any combination v-rescale, NHC, Langevin versus PR or MTTK is,<br>
> in priciple, right.<br>
><br>
><br>
> Maybe convergence speed changes, but in this case banchmark are quite<br>
> useful very welcolme!<br>
><br>
><br>
> best,<br>
> Francesco<br>
><br>
><br>
><br>
> > best<br>
> > Albert<br>
> > --<br>
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> --<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>
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><br>
><br>
><br>
><br>
> --<br>
> Cordiali saluti, Dr.Oteri Francesco<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>
<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>