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Hi,<br><br>This issue has been resolved.<br>It was indeed a problem of a pull group consisting of multiple molecules.<br>In this case the choice of the pull_pbcatom mdp parameter was critical.<br>If you do not set this, it takes the numerically middle atom of the group.<br>In this case that was an atom in a lipid head group.<br>The distance of this reference head group atom to the head groups<br>on the other side of the bilayer was shorter through pbc and the solvent<br>than through the bilayer.<br>Setting pull_pbcatom by hand to a tail end atom resolved the issue.<br><br>Berk<br><br><hr id="stopSpelling">From: gmx3@hotmail.com<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>Date: Wed, 28 Jan 2009 10:45:33 +0100<br><br>
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Hi,<br><br>You can mail the system to me.<br>Please include all the details required to run the system<br>and the different results you get with the exact Gromacs version numbers.<br><br>Berk<br><br>> Date: Wed, 28 Jan 2009 00:52:06 -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>> The permeants in my bilayer system are improperly pulled in calculations <br>> using all versions of Gromacs 4.0.x including the VERSION <br>> 4.0.99_development_20090120. Since, due to restrictions, I can not <br>> provide the topology file for my system to bugzilla, I constructed a <br>> similar prototypical system using Prof. Tieleman's POPC bilayer <br>> coordinates and field parameters. A buckyball permenat doped in the <br>> center of this system did indeed react similarly in a 4.0.3 calculation <br>> with an improper pull away from the equilibrated 3.3.1 constraint force <br>> coordinates. It was heartening to see that this problem was fixed for <br>> that system, by using VERSION 4.0.99_development_20090120. <br>> Unfortunately, again the problem remained for my actual system, even <br>> with use of the newest version of code.<br>> <br>> Since the cylinder option is now operational, I have a viable <br>> work-around for this problem. I am quite appreciative of the attention <br>> that this issue has received. If there is continued interest, and a <br>> willingness for an engineer to receive the topology file in a less <br>> public forum than bugzilla, I believe we could proceed with the <br>> debugging process.<br>> <br>> Thank you,<br>> <br>> Steve Fiedler<br>> <br>> <br>> <br>> <br>> Berk Hess wrote:<br>> > Hi,<br>> ><br>> > Just to be sure, the pull code is producing the correct results now?<br>> > The only problems should be in several analysis tools.<br>> ><br>> > The analysis tools have been written only with analysis of molecules<br>> > or parts of molecules in mind. When you want to analyze groups<br>> > that cover two molecules or more there will be pbc problems.<br>> > These are not simple to fix. If the distances between all the atoms<br>> > in the group are less than half a box length there is a unique COM.<br>> > The procedure should be similar to what trjconv -pbc cluster does.<br>> ><br>> > I can try to implement this for g_traj and g_dist.<br>> > Are there other tools that cause problems?<br>> ><br>> > Berk<br>> ><br>> > > Date: Mon, 26 Jan 2009 17:46:26 -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 Chris,<br>> > ><br>> > > Your suggestions were helpful. Due to the nature of this problem, there<br>> > > were limitations in the application of the sequence of steps that you<br>> > > recommended. Specifically, the difference in the equilibrated structure<br>> > > from version 3.3.x to the calculated reference center of mass from<br>> > > version 4.0.x causes an unreasonable "jump" with constraint force<br>> > > calculation. Resultant bad contacts prohibit generation of a pull<br>> > > output file.<br>> > ><br>> > > More generally though, I believe I understand your broader point: the<br>> > > sensitive nature of the periodic box with respect to the pull code and<br>> > > possible discrepancies in the pbc treatment by various utilities, may<br>> > > cause confusion with the diagnostic process. The test bilayer system I<br>> > > created however, centered distantly from the x and y box edges, may<br>> > > effectively remove this set of concerns. For example, this<br>> > > configuration is relatively unchanged upon "recentering", however it is<br>> > > still susceptible to the problem that is the subject of this discussion.<br>> > ><br>> > > If I can reproduce this phenomenon with a publicly available topology<br>> > > file, I can provide the necessary input files for inspection.<br>> > ><br>> > > Thank you again,<br>> > ><br>> > > Steve Fiedler<br>> > ><br>> > ><br>> > ><br>> > > chris.neale@utoronto.ca wrote:<br>> > > > Hi Steve,<br>> > > ><br>> > > > what I intended to suggest was actually something different (and much<br>> > > > easier).<br>> > > ><br>> > > > The idea is not that you need some special system to be able to<br>> > > > utilize the pull code, but that the pull code is correct whereas the<br>> > > > g_dist and g_traj programs are not as good at treating pbc in the way<br>> > > > that one desires.<br>> > > ><br>> > > > I suggest the following.<br>> > > ><br>> > > > 1. Take your original system and run the pull code for a very short<br>> > > > simulation. Use the last line of the output to calculate the relevant<br>> > > > displacement<br>> > > ><br>> > > > 2. Now use trjconv -b -e to get the last frame of the .xtc that<br>> > > > resulted from that short MD run as a .gro file, call it final.gro. I<br>> > > > suspect that your groups are not entirely in the same simulation box<br>> > > > in final.gro.<br>> > > ><br>> > > > 3. Now make a new .ndx file from that .gro and give it a single<br>> > > > residue that is near your binding pocket, call it R_1<br>> > > ><br>> > > > 4. Now apply trjconv -center -pbc mol -ur compact while selecting R_1<br>> > > > for centering, call the new .gro file final_center.gro<br>> > > ><br>> > > > 5. Visualize final_center.gro and ensure that all of your relevant<br>> > > > atoms are in the same image in the way that puts the minimum distance<br>> > > > between them along a path that is entirely contained within the unit<br>> > > > cell. If not, go back to step 3 and try making a group R_2, etc.<br>> > > > until this process works. NOTE: you might think that giving trjconv<br>> > > > -center the relevant groups that you use for pulling will be a good<br>> > > > idea here, but it is not. The problem there is that the atoms may be<br>> > > > "centered" by placing half on the left boundary and half on the right<br>> > > > boundary. I find using one logically selected residue or atom is the<br>> > > > best method here.<br>> > > ><br>> > > > 6. Assuming that you got what you wanted in step 5, now run g_traj <br>> > and<br>> > > > g_dist on final_center.gro. In my case, I found that g_traj and <br>> > g_dist<br>> > > > give the same answer as the pull code output when I am using<br>> > > > final_center.gro, but not always when I am using final.gro.<br>> > > ><br>> > > > *** I always laugh when these problems arise because, in an important<br>> > > > sense, the protein *did* jump out of the simulation box... at <br>> > least as<br>> > > > far as g_traj and g_dist are concerned. This, we must hope, is<br>> > > > correctly treated in the pull code even though it is incorrectly (or<br>> > > > at least unintuitively) treated by g_traj and g_dist.<br>> > > ><br>> > > > Chris.<br>> > > ><br>> > > > -- original message --<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 <br>> > 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 where g_traj and g_dist fail to give me the same distance<br>> > > >> as I obtain from the pull pos.xvg file. As Berk suggests, once I<br>> > > >> first trjconv -center -pbc mol -ur compact (giving an appropriate<br>> > > >> residue for centering that puts all relevant pulled atoms in the <br>> > same<br>> > > >> box) then g_traj and g_dist both give me the exact same answer as I<br>> > > >> calculate based on pull pos.xvg. Chris -- original message -- Hi,<br>> > > >> There could be a problem with periodic boundary conditions. Do you<br>> > > >> have multiple molecules in a pull group, or broken molecules? In <br>> > that<br>> > > >> case the COM position of 3.3.3 and g_traj are both incorrect. The<br>> > > >> pull code in 4.0 grompp and mdrun are (as far as I know) always<br>> > > >> correct. Berk<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 thewww<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>> > What can you do with the new Windows Live? Find out <br>> > <http://www.microsoft.com/windows/windowslive/default.aspx><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>> 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/">MSN Messenger</a><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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