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<br><br>> Date: Tue, 1 Sep 2009 09:45:35 -0500<br>> Subject: Re: [gmx-users] PMF using umbrella sampling<br>> From: bobjohnson1981@gmail.com<br>> To: gmx-users@gromacs.org<br>> <br>> Can you use runtype=constraint in parallel? I switched to using<br>> runtype=umbrella because I received error messages that the<br>> constraints can't be run in parallel.<br><br>With 3.3 you can not (or you actually could if you have both<br>groups on cpu 0 and remove the error).<br>With 4.0.5 the complete pull code works properly in parallel.<br><br>Berk<br><br>> <br>> Also...yes...I switched up angstroms and nanometers...I don't know how<br>> many times I've made that mistake and couldn't find it myself...<br>> <br>> Thanks,<br>> Bob<br>> <br>> On Tue, Sep 1, 2009 at 2:34 AM, Berk Hess<gmx3@hotmail.com> wrote:<br>> > Hi,<br>> ><br>> > Firstly, you are not constraining (runtype=constraint), but using a harmonic<br>> > umbrella potential.<br>> ><br>> > Secondly, your distance of 28.9 nm seems enormous, maybe you mixed<br>> > up nanometers and Angstroms here?<br>> ><br>> > Thirdly, I would strongly suggest to switch to Gromacs 4.0.5.<br>> > I have completely rewritten the pull code for Gromacs 4<br>> > and things now work much easier and better.<br>> ><br>> > Berk<br>> ><br>> >> Date: Mon, 31 Aug 2009 12:18:06 -0500<br>> >> From: bobjohnson1981@gmail.com<br>> >> To: gmx-users@gromacs.org<br>> >> Subject: [gmx-users] PMF using umbrella sampling<br>> >><br>> >> Hello everyone,<br>> >> I'm trying to compute the PMF for pulling two proteins apart. I'm<br>> >> planning on setting up several runs where the COM separation of the<br>> >> proteins is constrained and the constraint force is measured over the<br>> >> course of a long simulation. However, I'm having trouble doing this<br>> >> because I'm unsure of the inputs in the .ppa file. I'm trying to do<br>> >> this with Gromacs 3.3.3. Here is the .ppa file I'm using:<br>> >><br>> >> runtype = umbrella<br>> >> ngroups = 1<br>> >> reference_group = knob<br>> >> reftype = com<br>> >> pulldim = Y Y Y<br>> >> group_1 = car<br>> >> k1 = 1000<br>> >> pos1 = 0.0 0.0 28.8989219666<br>> >><br>> >> Here, there are two proteins: car and knob. The COM of car is located<br>> >> at (0.0 0.0 28.8989219666) relative to knob. The problem I'm<br>> >> experiencing is that the simulation results in the two proteins being<br>> >> pulled apart instead of constrained at distance pos1. I believe that<br>> >> I'm misinterpreting the inputs. Does anyone know the solution?<br>> >> Thanks,<br>> >> Bob<br>> >> _______________________________________________<br>> >> gmx-users mailing list gmx-users@gromacs.org<br>> >> http://lists.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>> > ________________________________<br>> > What can you do with the new Windows Live? Find out<br>> > _______________________________________________<br>> > gmx-users mailing list gmx-users@gromacs.org<br>> > http://lists.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>> <br>> <br>> <br>> -- <br>> Bob Johnson, PhD<br>> Institute for Computational Molecular Science<br>> Temple University<br>> 1900 North 12th Street<br>> Philadelphia, PA 19122<br>> http://www.sas.upenn.edu/~robertjo<br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.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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