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Hi,<br><br>There could be a problem with periodic boundary conditions.<br>Do you have multiple molecules in a pull group, or broken molecules?<br>In that case the COM position of 3.3.3 and g_traj are both incorrect.<br>The pull code in 4.0 grompp and mdrun are (as far as I know) always correct.<br><br>Berk<br><br>> Date: Thu, 22 Jan 2009 13:22:24 -0500<br>> From: fiedler@umich.edu<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance<br>> <br>> Dear all,<br>> <br>> I have encountered an odd behavior with use of the "pull_geometry = <br>> distance" option of the pull code, upon transitioning from Gromacs <br>> version 3.3.3 to version 4.0.3. It appears to be related to the center <br>> of mass distances of the two pull groups, which has an effect of <br>> abruptly displacing the coordinates of the less massive group. A <br>> diagnostic is a discrepancy between the distances between the pull <br>> groups from the preprocessor output in version 4.0.3, and the distance <br>> between the groups as calculated using the difference of the groups' <br>> centers of mass from the g_traj utility. For example, using the <br>> coordinates of a system previously equilibrated with the constraint <br>> force approach from version 3.3.3, the grompp output from version 4.0.3 is:<br>> <br>> Pull group natoms pbc atom distance at start reference at t=0<br>> 0 2672 1336 <br>> 1 60 6818 2.673 0.400 <br>> <br>> Using g_traj (4.0.3 version), the difference of the distance between the <br>> center of masses of the two groups is: 0.39911 nm versus the 2.673 value <br>> from above. <br>> <br>> This issue does not exist in previous versions of Gromacs including <br>> version 3.3.3. In version 4.0.3, this behavior occurs for both <br>> pull=umbrella and pull = constraint, on 32 and 64 bit architecture <br>> systems, and in both single and double precision calculations. A test <br>> of a two atom system determined that the pull_start option was not <br>> appropriate. The pull options used in the mdp file are listed below, as <br>> well as the contents of the ppa file which has worked previously. <br>> <br>> Suggestions would be appreciated,<br>> <br>> Thank you,<br>> <br>> Steve Fiedler<br>> <br>> Gromacs 4.0.0 mdp pull options<br>> pull = constraint<br>> pull_geometry = distance<br>> pull_dim = N N Y<br>> pull_start = no<br>> pull_init1 = .4<br>> pull_group0 = Ref<br>> pull_group1 = Buk<br>> <br>> Gromacs 3.3.3 ppa file:<br>> runtype = constraint<br>> group_1 = BUK<br>> reference_group = Ref<br>> reftype = com <br>> constraint_direction = 0 0 1<br>> constraint_distance1 = 0.400<br>> <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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