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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 /><hr />What can you do with the new Windows Live? <a href='http://www.microsoft.com/windows/windowslive/default.aspx' target='_new'>Find out</a></body>
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