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Hi,<br><br>Just to be 100% I also ran a simulation with pull rate 0.01 nm/ps.<br>In this case the pull velocity is smaller than the noise in the COM velocity.<br>But it is still there, the average velocity is + and - 0.005 nm/ps,<br>as one would expect. And integrating the velocity gives the poper displacement.<br><br>Berk<br><br><hr id="stopSpelling">From: gmx3@hotmail.com<br>To: gmx-users@gromacs.org<br>Subject: RE: [gmx-users] direction_periodic<br>Date: Thu, 1 Oct 2009 14:30:57 +0200<br><br>
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Hi,<br><br>I ran the initial part of the 0.1 nm/ps simulation again (since I deleted the 1 GB trr file).<br>I get fluctuating velocities for both groups around + and - 0.05 nm/ps with an<br>(initial) amplitude of the oscillation of 0.02 nm/ps.<br>This is exactly what you would expect.<br><br>Berk<br><br>> Date: Thu, 1 Oct 2009 14:08:28 +0200<br>> From: alexander.herz@mytum.de<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] direction_periodic<br>> <br>> Hi,<br>> <br>> did you look at the actual trajectory (trr/xtc) or the velocity of one<br>> of the diamond slabs (using g_traj) ?<br>> I do get a sawtooth style COM distance (pullx.xvg) but both the<br>> veloc.xvg and the trajectory show that the slabs are not actually moving<br>> much (the speed of the slab fluctuates wildly around 5e-3nm/ps in a<br>> 2500ps run when I'm pulling with 0.01nm/ps).<br>> <br>> Alex<br>> <br>> Berk Hess schrieb:<br>> > Hi,<br>> ><br>> > I just ran a simulation with your input files.<br>> > I only changed the geometry to direction_periodic and increased the<br>> > rate to 0.1.<br>> > The distance decreases linearly with a slight waviness due to the<br>> > harmonic potential.<br>> > The location of the reference group shows a sawtooth profile,<br>> > as one would expect in a periodic system.<br>> ><br>> > So it seems to work fine for me.<br>> ><br>> > Berk<br>> ><br>> > > Date: Thu, 1 Oct 2009 10:24:54 +0200<br>> > > From: alexander.herz@mytum.de<br>> > > To: gmx-users@gromacs.org<br>> > > Subject: Re: [gmx-users] direction_periodic<br>> > ><br>> > > Hey,<br>> > ><br>> > > did you find the time to look at it?<br>> > ><br>> > > Thx,<br>> > > Alex<br>> > ><br>> > > Berk Hess schrieb:<br>> > > > I am not sure I continued the simulation long enough.<br>> > > > I'll run it again tomorrow.<br>> > > ><br>> > > > Berk<br>> > > ><br>> > > > > Date: Mon, 28 Sep 2009 16:57:19 +0200<br>> > > > > From: alexander.herz@mytum.de<br>> > > > > To: gmx-users@gromacs.org<br>> > > > > Subject: Re: [gmx-users] direction_periodic<br>> > > > ><br>> > > > > Well..they do move forward for a few ps and then they move back<br>> > (they<br>> > > > > oscillate).<br>> > > > > Did you check for a longer period?<br>> > > > ><br>> > > > > Alex<br>> > > > ><br>> > > > > Berk Hess schrieb:<br>> > > > > > Strange...<br>> > > > > > I tested the code on the files you sent me<br>> > > > > > and the slabs were moving smoothly.<br>> > > > > ><br>> > > > > > Berk<br>> > > > > ><br>> > > > > > > Date: Mon, 28 Sep 2009 15:40:16 +0200<br>> > > > > > > From: alexander.herz@mytum.de<br>> > > > > > > To: gmx-users@gromacs.org<br>> > > > > > > Subject: Re: [gmx-users] direction_periodic<br>> > > > > > ><br>> > > > > > > Hey,<br>> > > > > > ><br>> > > > > > > so using the new direction_periodic with some kernels that<br>> > > > actually work<br>> > > > > > > and the sources from the git (unmodified)<br>> > > > > > > gives a nice smooth pull force but no actual mean displacement<br>> > > > of the<br>> > > > > > > groups to be pulled (on average they just stay where they<br>> > are,see<br>> > > > > > > attached graph). I'm still trying to pull them into opposite<br>> > > > directions<br>> > > > > > > though.<br>> > > > > > ><br>> > > > > > > I'm using this setup:<br>> > > > > > > pull = umbrella<br>> > > > > > > pull_geometry = direction_periodic<br>> > > > > > > pull_ngroups = 1<br>> > > > > > > pull_group0 = DIAM<br>> > > > > > > pull_group1 = DIAM2<br>> > > > > > > pulldim = Y N N<br>> > > > > > > pull_k1 = 1000.0<br>> > > > > > > pull_rate1 = 0.01<br>> > > > > > > pull_vec1 = -1.0 0.0 0.0<br>> > > > > > ><br>> > > > > > > How can I make the two diamond slabs actually move in opposite<br>> > > > > > > directions rather than just oscillating around their<br>> > > > > > > initial positions?<br>> > > > > > ><br>> > > > > > > Thx,<br>> > > > > > > Alex<br>> > > > > > ><br>> > > > > > > Berk Hess schrieb:<br>> > > > > > > > Hi,<br>> > > > > > > ><br>> > > > > > > > Don't use fortran.<br>> > > > > > > > We will get rid of it before the 4.1 release.<br>> > > > > > > ><br>> > > > > > > > Berk<br>> > > > > > > ><br>> > > > > > > > > Date: Mon, 21 Sep 2009 16:17:17 +0200<br>> > > > > > > > > From: alexander.herz@mytum.de<br>> > > > > > > > > To: gmx-users@gromacs.org<br>> > > > > > > > > Subject: Re: [gmx-users] direction_periodic<br>> > > > > > > > ><br>> > > > > > > > > Hey,<br>> > > > > > > > ><br>> > > > > > > > > ok, I checked this. It works ok with the assembly<br>> > kernels on my<br>> > > > > > local<br>> > > > > > > > > machine, but it fails with fortran kernels<br>> > > > > > > > > on the HPC and on my local machine.<br>> > > > > > > > ><br>> > > > > > > > > Alex<br>> > > > > > > > ><br>> > > > > > > > > Berk Hess schrieb:<br>> > > > > > > > > > Yes.<br>> > > > > > > > > ><br>> > > > > > > > > > Berk<br>> > > > > > > > > ><br>> > > > > > > > > > > Date: Mon, 21 Sep 2009 14:42:43 +0200<br>> > > > > > > > > > > From: alexander.herz@mytum.de<br>> > > > > > > > > > > To: gmx-users@gromacs.org<br>> > > > > > > > > > > Subject: Re: [gmx-users] direction_periodic<br>> > > > > > > > > > ><br>> > > > > > > > > > > With master branch you mean the code I get via<br>> > > > > > > > > > ><br>> > > > > > > > > > > |git clone git://git.gromacs.org/gromacs.git<br>> > > > > > > > > > ><br>> > > > > > > > > > > right?<br>> > > > > > > > > > ><br>> > > > > > > > > > > Alex<br>> > > > > > > > > > > |<br>> > > > > > > > > > ><br>> > > > > > > > > > ><br>> > > > > > > > > > ><br>> > > > > > > > > > > Berk Hess schrieb:<br>> > > > > > > > > > > > I tested on your system and got good results.<br>> > > > > > > > > > > > There is still a tricky issue: the pull COM is still<br>> > > > > > determined<br>> > > > > > > > > > > > in the "standard" way by summing distances from the<br>> > > > pbcatom.<br>> > > > > > > > > > > > Therefore atoms should not change nearest image<br>> > from he<br>> > > > > > pbcatom.<br>> > > > > > > > > > > > This would result in nasty noise in the pull COM and<br>> > > > force.<br>> > > > > > > > > > > ><br>> > > > > > > > > > > > I would suggest that you try to run the master<br>> > branch and<br>> > > > > > check<br>> > > > > > > > > > > > if that works.<br>> > > > > > > > > > > ><br>> > > > > > > > > > > > Berk<br>> > > > > > > > > > > ><br>> > > > > > > > > > > > > Date: Mon, 21 Sep 2009 14:31:34 +0200<br>> > > > > > > > > > > > > From: alexander.herz@mytum.de<br>> > > > > > > > > > > > > To: gmx-users@gromacs.org<br>> > > > > > > > > > > > > Subject: [gmx-users] direction_periodic<br>> > > > > > > > > > > > ><br>> > > > > > > > > > > > > Hey,<br>> > > > > > > > > > > > ><br>> > > > > > > > > > > > > after some pain of merging the dev branch into<br>> > our 4.0.5<br>> > > > > > version<br>> > > > > > > > > > I got<br>> > > > > > > > > > > > > the new pull mode "direction_periodic"<br>> > > > > > > > > > > > > running over the weekend. There's some weird<br>> > > > rotation of the<br>> > > > > > > > pulled<br>> > > > > > > > > > > > > objects going on and pbc seem weird as well (there<br>> > > > are water<br>> > > > > > > > > > molecules<br>> > > > > > > > > > > > > in those positions where I'd expect the periodic<br>> > > > image of my<br>> > > > > > > > diamond<br>> > > > > > > > > > > > > slab which leaves the box at one side). I guess you<br>> > > > > > tested the<br>> > > > > > > > > > new pull<br>> > > > > > > > > > > > > mode somehow, so any ideas what's going on here? I'm<br>> > > > still<br>> > > > > > > > trying to<br>> > > > > > > > > > > > > perform the same experiment for which I send you the<br>> > > > > > input files<br>> > > > > > > > > > while<br>> > > > > > > > > > > > > ago and for which you kindly implemented the new<br>> > > > pull mode.<br>> > > > > > > > > > > > ><br>> > > > > > > > > > > > > Thx for your help,<br>> > > > > > > > > > > > > Alex<br>> > > > > > > > > > > > ><br>> > > > > > > > > > > > > Berk Hess schrieb:<br>> > > > > > > > > > > > > > I have committed a new pull geometry<br>> > > > direction_periodic to<br>> > > > > > > > the git<br>> > > > > > > > > > > > > > master branch. It is not documented yet.<br>> > > > > > > > > > > > > > It works the same at direction, but allows<br>> > > > distances to be<br>> > > > > > > > larger<br>> > > > > > > > > > > > > > than half the box and does not add the pull force<br>> > > > to the<br>> > > > > > > > virial.<br>> > > > > > > > > > > > > ><br>> > > > > > > > > > > > > > Berk<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<br>> > > > http://www.gromacs.org/search<br>> > > > > > > > before<br>> > > > > > > > > > > > posting!<br>> > > > > > > > > > > > > Please don't post (un)subscribe requests to the<br>> > list.<br>> > > > > > Use the<br>> > > > > > > > > > > > > www interface or send it to<br>> > > > gmx-users-request@gromacs.org.<br>> > > > > > > > > > > > > Can't post? Read<br>> > > > > > http://www.gromacs.org/mailing_lists/users.php<br>> > > > > > > > > > > ><br>> > > > > > > > > > > ><br>> > > > > > > > > ><br>> > > > > > > ><br>> > > > > ><br>> > > ><br>> > ------------------------------------------------------------------------<br>> > > > > > > > > > > > Express yourself instantly with MSN Messenger! MSN<br>> > > > Messenger<br>> > > > > > > > > > > ><br>> > <http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/><br>> > > > > > > > > > > ><br>> > > > > > > > > ><br>> > > > > > > ><br>> > > > > ><br>> > > ><br>> > ------------------------------------------------------------------------<br>> > > > > > > > > > > ><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<br>> > http://www.gromacs.org/search<br>> > > > > > before<br>> > > > > > > > > > posting!<br>> > > > > > > > > > > > Please don't post (un)subscribe requests to the list.<br>> > > > Use the<br>> > > > > > > > > > > > www interface or send it to<br>> > gmx-users-request@gromacs.org.<br>> > > > > > > > > > > > Can't post? Read<br>> > > > > > http://www.gromacs.org/mailing_lists/users.php<br>> > > > > > > > > > ><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<br>> > http://www.gromacs.org/search<br>> > > > > > before<br>> > > > > > > > > > posting!<br>> > > > > > > > > > > Please don't post (un)subscribe requests to the list.<br>> > > > Use the<br>> > > > > > > > > > > www interface or send it to<br>> > gmx-users-request@gromacs.org.<br>> > > > > > > > > > > Can't post? Read<br>> > > > http://www.gromacs.org/mailing_lists/users.php<br>> > > > > > > > > ><br>> > > > > > > > > ><br>> > > > > > > ><br>> > > > > ><br>> > > ><br>> > ------------------------------------------------------------------------<br>> > > > > > > > > > Express yourself instantly with MSN Messenger! MSN<br>> > Messenger<br>> > > > > > > > > > <http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/><br>> > > > > > > > > ><br>> > > > > > > ><br>> > > > > ><br>> > > ><br>> > ------------------------------------------------------------------------<br>> > > > > > > > > ><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<br>> > > > before<br>> > > > > > > > posting!<br>> > > > > > > > > > Please don't post (un)subscribe requests to the list.<br>> > Use the<br>> > > > > > > > > > www interface or send it to gmx-users-request@gromacs.org.<br>> > > > > > > > > > Can't post? Read<br>> > > > http://www.gromacs.org/mailing_lists/users.php<br>> > > > > > > > ><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<br>> > > > before<br>> > > > > > > > posting!<br>> > > > > > > > > Please don't post (un)subscribe requests to the list.<br>> > Use the<br>> > > > > > > > > www interface or send it to gmx-users-request@gromacs.org.<br>> > > > > > > > > Can't post? Read<br>> > http://www.gromacs.org/mailing_lists/users.php<br>> > > > > > > ><br>> > > > > > > ><br>> > > > > ><br>> > > ><br>> > ------------------------------------------------------------------------<br>> > > > > > > > Express yourself instantly with MSN Messenger! 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MSN Messenger<br>> > > > > > <http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/><br>> > > > > ><br>> > > ><br>> > ------------------------------------------------------------------------<br>> > > > > ><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<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>> > > > > 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<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>> > > > <http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/><br>> > > ><br>> > ------------------------------------------------------------------------<br>> > > ><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<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>> > > 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<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>> > See all the ways you can stay connected to friends and family<br>> > <http://www.microsoft.com/windows/windowslive/default.aspx><br>> > ------------------------------------------------------------------------<br>> ><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>> 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/">MSN Messenger</a> <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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