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Hi,<br><br>Strange, I think I have really fixed all problems now.<br>All test systems work fine for me.<br><br>Can you file a bugzilla entry?<br>Please include all the files needed to run grompp<br>as well as the correct pull distance and the pull distance you obtained.<br><br>Berk<br><br>> Date: Sun, 25 Jan 2009 23:45:29 -0500<br>> From: fiedler@umich.edu<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance<br>> <br>> Hi,<br>> <br>> I rebuilt the code using both sets of Berk's corrections. On an <br>> isolated bilayer system with no periodic boundaries in the x-y plane <br>> prepared in the manner previously explained, the recompiled grompp <br>> output yielded no improvement in the discrepancies of the position of a <br>> buckyball permeant. By visual inspection, it appears that the 4.0.x <br>> versions still attempt to distort the position of the permeant <br>> significant upward from the bilayer center, i.e., the center of mass of <br>> the reference group. Interestingly, the 3.3.x and 4.0.x version <br>> identically treated a test bilayer system constructed with a single <br>> dummy particle permeant. <br>> <br>> I appreciate the help of Berk, and Chris' detailed suggestions with this <br>> interesting problem.<br>> <br>> Sincerely,<br>> <br>> Steve Fiedler<br>> <br>> <br>> <br>> Berk Hess wrote:<br>> > Hi,<br>> ><br>> > I just found out that I introduced a bug in 4.0.3, which could cause<br>> > the pull code to crash or give wrong results when running single <br>> > processor.<br>> > In parallel it is correct.<br>> > I committed fixed for 4.0.4.<br>> ><br>> > If you run in parallel things should be correct,<br>> > or change in src/kernel/md.c:<br>> > if (ir->pull) {<br>> > dd_make_local_pull_groups(NULL,ir->pull,mdatoms);<br>> > to<br>> > if (ir->pull && PAR(cr)) {<br>> > dd_make_local_pull_groups(NULL,ir->pull,mdatoms);<br>> ><br>> > Berk<br>> ><br>> > > Date: Fri, 23 Jan 2009 12:14:43 -0500<br>> > > From: fiedler@umich.edu<br>> > > To: gmx-users@gromacs.org<br>> > > Subject: Re: [gmx-users] Transition difficulties: version 3.3.3 to <br>> > 4.0.3 regarding pull_geometry=distance<br>> > ><br>> > > Hi,<br>> > ><br>> > > Thank you Berk and Chris for the suggestions.<br>> > ><br>> > > To address the possibility that this issue is related to periodic<br>> > > boundaries, I used two approaches:<br>> > > 1. The pull group of interest (permeant) was centered in the x-y plane<br>> > > of the box using Chris' approach. I then used the genconf utility to<br>> > > replicate my lipid box to a 9x9 grid in the x-y plane and removed all<br>> > > but the center box. This generated the coordinates for a bilayer system<br>> > > with all lipid molecules inside a box and intact. The discrepancy<br>> > > between the grompp (version 4.0.3) output and distances as <br>> > calculated by<br>> > > g_traj (version 4.0.3) persist, 2.667 vs. 0.3996 nm.<br>> > > 2. I constructed a three atom system containing 2 reference atoms of<br>> > > type A, and a "pull" atom of type B. Proper output from grompp was<br>> > > observed for all coordinates of both the reference and pulled atoms,<br>> > > include coordinates for atoms moved outside the box in the x-y plane.<br>> > > The coordinate, topology, and run control parameter file are given <br>> > below.<br>> > ><br>> > > If there are additional suggestions, I would be greatly appreciative.<br>> > ><br>> > > Thank you,<br>> > ><br>> > > Steve Fiedler<br>> > ><br>> > > -----------------<br>> > > conf.gro<br>> > > Three atoms<br>> > > 3<br>> > > 1AAA A 1 1.500 1.500 1.000<br>> > > 2AAA A 2 0.500 1.500 1.000<br>> > > 3BBB B 3 -1.500 1.500 1.700<br>> > > 3.00000 3.00000 3.00000<br>> > > -----------------<br>> > > index.ndx<br>> > > [ System ]<br>> > > 1 2 3<br>> > > [ Ref ]<br>> > > 1 2<br>> > > [ Pulled ]<br>> > > 3<br>> > > -----------------<br>> > > grompp.mdp<br>> > > title = ThreeAtoms<br>> > > integrator = md<br>> > > dt = 0.001<br>> > > nsteps = 1<br>> > > ns_type = grid<br>> > > pbc = xyz<br>> > > coulombtype = shift<br>> > > rlist = 1.4<br>> > > rcoulomb = 1.4<br>> > > rvdw = 1.4<br>> > > tcoupl = no<br>> > > pcoupl = no<br>> > > constraint_algorithm = shake<br>> > > shake_tol = 1e-4<br>> > > gen-vel = no<br>> > > gen-temp = 0<br>> > ><br>> > > nstxout = 1<br>> > > nstvout = 0<br>> > > nstfout = 0<br>> > ><br>> > > pull = umbrella<br>> > > pull_geometry = distance<br>> > > pull_dim = N N Y<br>> > > pull_start = no<br>> > > pull_init1 = 0.7<br>> > > pull_group0 = Ref<br>> > > pull_group1 = Pulled<br>> > > pull_k1 = 10000<br>> > > -----------------<br>> > > topology.top<br>> > > ; topology for two partially charged atoms<br>> > ><br>> > > [ defaults ]<br>> > > ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ<br>> > > 1 3 yes 0.125 0.5<br>> > ><br>> > > [ atomtypes ]<br>> > > ;name mass charge ptype sig eps<br>> > > A 1000.0000 0.000 A 0.50000 9.90000<br>> > > B 9.0000 0.000 A 0.30000 9.00000<br>> > ><br>> > > [ nonbond_params ]<br>> > > ; i j func sig eps<br>> > ><br>> > > [ moleculetype ]<br>> > > AAAA 1<br>> > ><br>> > > [ atoms ]<br>> > > ; nr type resnr residue atom cgnr charge mass<br>> > > 1 A 1 AAA A 1 0.000 1000.0000<br>> > ><br>> > > [ moleculetype ]<br>> > > BBBB 1<br>> > ><br>> > > [ atoms ]<br>> > > ; nr type resnr residue atom cgnr charge mass<br>> > > 1 B 1 BBB B 1 0.000 9.00<br>> > ><br>> > > [ system ]<br>> > > ; name<br>> > > Three atoms<br>> > ><br>> > > [ molecules ]<br>> > > ; name number<br>> > > AAAA 2<br>> > > BBBB 1<br>> > ><br>> > ><br>> > ><br>> > ><br>> > ><br>> > > Chris Neale wrote:<br>> > > > I just checked similar simulations of mine and Berk's suggestion<br>> > > > accounts for similar discrepancies that I notice on a quick <br>> > evaluation<br>> > > > where g_traj and g_dist fail to give me the same distance as I obtain<br>> > > > from the pull pos.xvg file. As Berk suggests, once I first trjconv<br>> > > > -center -pbc mol -ur compact (giving an appropriate residue for<br>> > > > centering that puts all relevant pulled atoms in the same box) then<br>> > > > g_traj and g_dist both give me the exact same answer as I calculate<br>> > > > based on pull pos.xvg. Chris -- original message -- Hi, There <br>> > could be<br>> > > > a problem with periodic boundary conditions. Do you have multiple<br>> > > > molecules in a pull group, or broken molecules? In that case the COM<br>> > > > position of 3.3.3 and g_traj are both incorrect. The pull code in 4.0<br>> > > > grompp and mdrun are (as far as I know) always correct. 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<br>> > > >> 4.0.3 regarding pull_geometry=distance<br>> > > >> > > Dear all,<br>> > > >> > > I have encountered an odd behavior with use of the <br>> > "pull_geometry<br>> > > >> = > distance" option of the pull code, upon transitioning from<br>> > > >> Gromacs > version 3.3.3 to version 4.0.3. It appears to be related<br>> > > >> to the center > of mass distances of the two pull groups, which has<br>> > > >> an effect of > abruptly displacing the coordinates of the less<br>> > > >> massive group. A > diagnostic is a discrepancy between the distances<br>> > > >> between the pull > groups from the preprocessor output in version<br>> > > >> 4.0.3, and the distance > between the groups as calculated using the<br>> > > >> difference of the groups' > centers of mass from the g_traj utility.<br>> > > >> For example, using the > coordinates of a system previously<br>> > > >> equilibrated with the constraint > force approach from version <br>> > 3.3.3,<br>> > > >> the grompp output from version 4.0.3 is:<br>> > > >> > > Pull group natoms pbc atom distance at start reference at t=0<br>> > > >> > 0 2672 1336 > 1 60 6818<br>> > > >> 2.673 0.400 > > Using g_traj (4.0.3 version), the<br>> > > >> difference of the distance between the > center of masses of the two<br>> > > >> groups is: 0.39911 nm versus the 2.673 value > from above. > > This<br>> > > >> 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<br>> > > >> test > of a two atom system determined that the pull_start option <br>> > was<br>> > > >> not > appropriate. The pull options used in the mdp file are listed<br>> > > >> below, as > well as the contents of the ppa file which has worked<br>> > > >> previously. > > Suggestions would be appreciated,<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 www<br>> > > > 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>> > ><br>> > > --<br>> > > Steve Fiedler, Ph.D.<br>> > > Research Fellow<br>> > > Department of Mechanical Engineering<br>> > > The University of Michigan<br>> > > 2024 G.G. Brown<br>> > > 2350 Hayward St.<br>> > > Ann Arbor, MI 48109-2125<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>> > Express yourself instantly with MSN Messenger! MSN Messenger <br>> > <http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/><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>> <br>> -- <br>> Steve Fiedler, Ph.D.<br>> Research Fellow<br>> Department of Mechanical Engineering<br>> The University of Michigan<br>> 2024 G.G. Brown<br>> 2350 Hayward St.<br>> Ann Arbor, MI 48109-2125<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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