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Hi,<br><br>If you pull without a reference, you will be doing nothing in the limit<br>of slow pulling. For fast pulling you will be doing something.<br><br>pull_start=yes<br>pull_init1=0<br>will initialize set pull_init to the initial distance.<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 19:59:38 +0300<br>> <br>> OK,<br>> <br>> finally I try to simplify my question by revealing my final aim.<br>> <br>> I have a group that I want to pull out of my protein. I want only one<br>> group to be pulled out in one direction. <br>> <br>> How could I do that?<br>> SDA<br>> <br>> P.S.<br>> In my understanding to do that I should leave reference group blank and<br>> specify pull group only:<br>> pull_group0=<br>> pull_group1=r_535<br>> In this case grompp calculates initial distance from (0,0,0) to pull<br>> group and sets the initial force to a very high value<br>> (distance*force_constant) instead of 0. To correct this and to make the<br>> initial pull rate = 0 I should set pull group to the center of<br>> coordinates or set the initial position of the pull spring to the<br>> position of the pull group. How should I do that?<br>> <br>> <br>> On Tue, 2009-01-13 at 16:55 +0100, Berk Hess wrote:<br>> > 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<br>> > 100<br>> > > ps - that is OK I suggest. The problem is that pull group<br>> > (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<br>> > stays<br>> > > intact to track the movement of the group that is being pulled -<br>> > pull<br>> > > group. Then how could this happen in my system? What should I do to<br>> > pull<br>> > > only the pull_group1?<br>> > > 2/ I was recomended to use AFM pull mode in gromacs 3. What is the<br>> > 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<br>> > 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>> > Express yourself instantly with MSN Messenger! MSN Messenger<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 />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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