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<body class='hmmessage'><div style="text-align: left;"><br></div><br><br><br><hr id="stopSpelling">> From: mihoopes@ucdavis.edu<br>> To: gmx-users@gromacs.org<br>> Subject: RE: [gmx-users] stochastic dynamics , langevin<br>> Date: Thu, 23 Oct 2008 15:32:02 -0700<br>> <br>> Along these same lines...<br>> (a)is there an thermostat setting in GROMACS that comes close to the DPD<br>> thermostat as described in (T. Soddemann, B. D¨unweg, and K. Kremer.<br>> Dissipative particle dynamics: A useful thermostat for equilibrium and<br>> nonequilibrium molecular dynamics simulations. Phys. Rev. E, 68:046702,<br>> 2003.)<br><br>No.<br><br>> (b) if nothing approaches DPD, how would a one go about starting to write a<br>> new thermostat in GROMACS?<br><br>Implementing a new thermostat in Gromacs is easy, except for DPD,<br>since it interferes both with the neighborlist and the integration.<br>I have considered implementing DPD, but it is a lot of work<br>and also difficult to do efficiently, since the DPD interactions are<br>more expensive that the Coulomb and LJ interactions.<br><br>Note that you only really need DPD for non-equilibrium phenomena<br>where hydrodynamics plays a role.<br><br>Berk<br><br><br>> <br>> -Matt<br>> <br>> ---------------------------------------------<br>> Matthew Hoopes<br>> Biophysics Graduate Group<br>> University of California, Davis<br>> <br>> mihoopes@ucdavis.edu<br>> 530-752-6452<br>> --------------------------------------------- <br>> <br>> <br>> Hi,<br>> <br>> Brownina dynamics is a Langevin equation for the coordinates (no inertia).<br>> Stochastic dynamics is a Langevin equation for the velocities (with<br>> inertia).<br>> <br>> Everything depends on what you want to do, which you do not tell in detail.<br>> If you want to leave out the solvent, but you want to simulate a system in<br>> solvent, SD is not going to help you, since there is no implicit solvent<br>> potential, so your potential and therefore your sampling is nonsense.<br>> <br>> tau_t has no effect on the distribution, only on the dynamics. If you want<br>> the correct dynamics, you will have fit tau_t to reproduce some kinetic<br>> quantity that you are interested in. For different quantities tau_t can be<br>> different.<br>> <br>> Berk<br>> <br>> <br>> Date: Thu, 23 Oct 2008 15:31:16 +0200<br>> From: omermar@gmail.com<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] stochastic dynamics , langevin<br>> <br>> Dear All,<br>> I am trying to perform Langevin dynamics of large peptides / proteins. After<br>> reading the manual & going over some old mails in this list, I have two<br>> points I hope you could clear for me:<br>> <br>> [Gromacs version 3.3.3]<br>> <br>> 1) I am a bit confused with Brownian vs. Langevin dynamics. Is this the<br>> proper keywords I should use for Langevin dynamics: integrator = sd ;<br>> <br>> bd-fric = 0 ;<br>> tau_t = 10 ;<br>> ref_t = 300 ;<br>> With bd-fric=0, the friction is taken as the inverse tau_t.<br>> <br>> <br>> 2) From your experience, what are good values of tau_t (or 1/tau_t) for<br>> simulating a protein? In 2006 list, David has commented that choosing tau_t<br>> is very important (<br>> http://www.gromacs.org/pipermail/gmx-users/2006-July/023089.html ).<br>> <br>> <br>> Your help is appreciated. Omer. <br>> Koby Levy research group,<br>> Weizmann Institute of Science. <br>> http://www.weizmann.ac.il/sb/faculty_pages/Levy/<br>> <br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br><br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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