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<body class='hmmessage'><div style="text-align: left;"><br></div><br><br><br><hr id="stopSpelling">> Date: Wed, 23 Apr 2008 06:56:32 -0700<br>> From: schneemilch@yahoo.com<br>> Subject: RE: [gmx-users] couette flow<br>> To: gmx-users@gromacs.org<br>> <br>> <br>> <br>> <br>> --- On Wed, 4/23/08, Berk Hess <gmx3@hotmail.com> wrote:<br>> <br>> > From: Berk Hess <gmx3@hotmail.com><br>> > Subject: RE: [gmx-users] couette flow<br>> > To: "Discussion list for GROMACS users" <gmx-users@gromacs.org><br>> > Date: Wednesday, April 23, 2008, 10:25 PM<br>> > > Date: Wed, 23 Apr 2008 05:29:26 -0700<br>> > > From: schneemilch@yahoo.com<br>> > > Subject: RE: [gmx-users] couette flow<br>> > > To: gmx3@hotmail.com<br>> > > <br>> > > <br>> > > <br>> > > <br>> > > --- On Wed, 4/23/08, Berk Hess<br>> > <gmx3@hotmail.com> wrote:<br>> > > <br>> > > > From: Berk Hess <gmx3@hotmail.com><br>> > > > Subject: RE: [gmx-users] couette flow<br>> > > > To: schneemilch@yahoo.com<br>> > > > Date: Wednesday, April 23, 2008, 7:27 PM<br>> > > > > Date: Wed, 23 Apr 2008 02:34:49 -0700<br>> > > > > From: schneemilch@yahoo.com<br>> > > > > To: gmx-users@gromacs.org<br>> > > > > Subject: [gmx-users] couette flow<br>> > > > > <br>> > > > > Hi,<br>> > > > > Has anyone here used gromacs to simulate<br>> > couette flows<br>> > > > in slit pores? I can see that it would be<br>> > possible to use<br>> > > > the pull code but I would like to be able to run<br>> > in<br>> > > > parallel. Any tips before I begin modifying<br>> > source code<br>> > > > would be greatly appreciated.<br>> > > > > <br>> > > > > Cheers, Matt<br>> > > > <br>> > > > I don't see what this has to do with the pull<br>> > code. The<br>> > > > pull code is made for forces between<br>> > > > centers of mass of groups.<br>> > > > <br>> > > > There are already some external force options in<br>> > the mdp<br>> > > > file.<br>> > > > <br>> > > > But I don't see how you would set up an<br>> > unbiased<br>> > > > couette flow.<br>> > > > In reality the flow is generated by a pressure<br>> > difference.<br>> > > > In a simulation you can apply an external force<br>> > or impose a<br>> > > > velocity profile.<br>> > > > But both these options make presumptions about<br>> > the<br>> > > > force/flow profile.<br>> > > > <br>> > > > Berk.<br>> > > > <br>> > > <br>> > > Couette flow is shear driven, all you need is to have<br>> > one pore wall moving relative to the other. I figure this<br>> > could be done using the pull code by assigning each wall to<br>> > a different group and using the pull code to increase the<br>> > lateral distance between them at a constant rate. But it<br>> > seems that the pull code does not work in parallel. Is<br>> > there another way to prescribe the motion of one of the<br>> > walls?<br>> > > Cheers, Matt<br>> > <br>> > Ah, sorry, I confused it with Poiseuille.<br>> > <br>> > The deform option does shear boundary conditions.<br>> > <br>> > But if you want to move real walls, there is currently no<br>> > simple option that gives<br>> > a group a constant velocity. The pull code should indeed do<br>> > it. In the CVS version<br>> > the pull code also works in parallel.<br>> > <br>> > BTW the reply address in your mail is your own address,<br>> > instead of gmx-users,<br>> > I don't you if you caused this, or if something is<br>> > wrong on the server.<br>> > <br>> > Berk.<br>> > <br>> > <br>> In that case I guess it would be easiest to switch to the CVS version. Thanks for the tip.<br>> Cheers, Matt<br><br>I just realized that this will probably not work.<br>I assume you have periodic walls. In that case one can not define a center of mass.<br><br>The easiest way is probably editing the code and use the accelerate group option in the mdp file.<br>It is not difficult to modify the update routine(s) in src/mdlib/update.c to apply a velocity<br>instead of an acceleration.<br><br>Another option would be to actually apply an acceleration to one of the walls and this will<br>then result in a certain shear rate.<br><br>Berk.<br><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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