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Hi,<br><br>The pull option acts between COM's. Both COM's will move.<br>If not, you would have a net force on the COM of the whole system.<br><br>The AFM option is no longer there.<br>I never understood what the difference between Umbrella and AFM was.<br>But Umbrella (as well as constraint) should be able to do all things<br>that were possible before (and more).<br><br>Berk<br><br>> Subject: Re: [gmx-users] Pull Code problems<br>> From: genesup@gmail.com<br>> To: gmx-users@gromacs.org<br>> Date: Tue, 13 Jan 2009 18:44:36 +0300<br>> <br>> OK,<br>> I have a new problem.<br>> I`ve started the simulation with the following pull parameters<br>> <br>> <br>> ;-----------PULL CODE ---------------------<br>> <br>> pull<-->=<-----> umbrella<br>> pull_geometry<->= direction<br>> pull_group0<-->= r_500<br>> pull_group1<--->= r_535<br>> pull_vec1<----->= -1.306 1.355 -0.319<br>> pull_k1><------>= 1000<br>> pull_rate1<---->= 1 ; nm/ps = 1 A/ns<br>> <br>> With such extreme pulling velocities I had my system teared apart in 100<br>> ps - that is OK I suggest. The problem is that pull group (pull_group1)<br>> and reference group (pull_group0) were both pulled in opposite<br>> directions - pull_vec1 and -(pull_vec1)?!<br>> <br>> 1/ In my best understanding the reference group is the one that stays<br>> intact to track the movement of the group that is being pulled - pull<br>> group. Then how could this happen in my system? What should I do to pull<br>> only the pull_group1?<br>> 2/ I was recomended to use AFM pull mode in gromacs 3. What is the new<br>> name for AFM in gromacs 4? <br>> <br>> Thanks.<br>> <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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