Dear Berk, I think that g_clustsize has a similar problem. IIRC I fixed it in a similar way on my own copy. There are probably other tools that will suffer from this as well, but for g_clustsize it's important because it may deal with such groups.
Same goes for trjconv, e.g., for a protein and ligand. Ran. Berk Hess wrote: > Hi, > > Just to be sure, the pull code is producing the correct results now? > The only problems should be in several analysis tools. > > The analysis tools have been written only with analysis of molecules > or parts of molecules in mind. When you want to analyze groups > that cover two molecules or more there will be pbc problems. > These are not simple to fix. If the distances between all the atoms > in the group are less than half a box length there is a unique COM. > The procedure should be similar to what trjconv -pbc cluster does. > > I can try to implement this for g_traj and g_dist. > Are there other tools that cause problems? > > Berk > > > Date: Mon, 26 Jan 2009 17:46:26 -0500 > > From: fied...@umich.edu > > To: gmx-users@gromacs.org > > Subject: Re: [gmx-users] Transition difficulties: version 3.3.3 to > 4.0.3 regarding pull_geometry=distance > > > > Hi Chris, > > > > Your suggestions were helpful. Due to the nature of this problem, there > > were limitations in the application of the sequence of steps that you > > recommended. Specifically, the difference in the equilibrated structure > > from version 3.3.x to the calculated reference center of mass from > > version 4.0.x causes an unreasonable "jump" with constraint force > > calculation. Resultant bad contacts prohibit generation of a pull > > output file. > > > > More generally though, I believe I understand your broader point: the > > sensitive nature of the periodic box with respect to the pull code and > > possible discrepancies in the pbc treatment by various utilities, may > > cause confusion with the diagnostic process. The test bilayer system I > > created however, centered distantly from the x and y box edges, may > > effectively remove this set of concerns. For example, this > > configuration is relatively unchanged upon "recentering", however it is > > still susceptible to the problem that is the subject of this discussion. > > > > If I can reproduce this phenomenon with a publicly available topology > > file, I can provide the necessary input files for inspection. > > > > Thank you again, > > > > Steve Fiedler > > > > > > > > chris.ne...@utoronto.ca wrote: > > > Hi Steve, > > > > > > what I intended to suggest was actually something different (and much > > > easier). > > > > > > The idea is not that you need some special system to be able to > > > utilize the pull code, but that the pull code is correct whereas the > > > g_dist and g_traj programs are not as good at treating pbc in the way > > > that one desires. > > > > > > I suggest the following. > > > > > > 1. Take your original system and run the pull code for a very short > > > simulation. Use the last line of the output to calculate the relevant > > > displacement > > > > > > 2. Now use trjconv -b -e to get the last frame of the .xtc that > > > resulted from that short MD run as a .gro file, call it final.gro. I > > > suspect that your groups are not entirely in the same simulation box > > > in final.gro. > > > > > > 3. Now make a new .ndx file from that .gro and give it a single > > > residue that is near your binding pocket, call it R_1 > > > > > > 4. Now apply trjconv -center -pbc mol -ur compact while selecting R_1 > > > for centering, call the new .gro file final_center.gro > > > > > > 5. Visualize final_center.gro and ensure that all of your relevant > > > atoms are in the same image in the way that puts the minimum distance > > > between them along a path that is entirely contained within the unit > > > cell. If not, go back to step 3 and try making a group R_2, etc. > > > until this process works. NOTE: you might think that giving trjconv > > > -center the relevant groups that you use for pulling will be a good > > > idea here, but it is not. The problem there is that the atoms may be > > > "centered" by placing half on the left boundary and half on the right > > > boundary. I find using one logically selected residue or atom is the > > > best method here. > > > > > > 6. Assuming that you got what you wanted in step 5, now run g_traj > and > > > g_dist on final_center.gro. In my case, I found that g_traj and > g_dist > > > give the same answer as the pull code output when I am using > > > final_center.gro, but not always when I am using final.gro. > > > > > > *** I always laugh when these problems arise because, in an important > > > sense, the protein *did* jump out of the simulation box... at > least as > > > far as g_traj and g_dist are concerned. This, we must hope, is > > > correctly treated in the pull code even though it is incorrectly (or > > > at least unintuitively) treated by g_traj and g_dist. > > > > > > Chris. > > > > > > -- original message -- > > > > > > Hi, > > > > > > Thank you Berk and Chris for the suggestions. > > > > > > To address the possibility that this issue is related to periodic > > > boundaries, I used two approaches: > > > 1. The pull group of interest (permeant) was centered in the x-y plane > > > of the box using Chris' approach. I then used the genconf utility to > > > replicate my lipid box to a 9x9 grid in the x-y plane and removed all > > > but the center box. This generated the coordinates for a bilayer > system > > > with all lipid molecules inside a box and intact. The discrepancy > > > between the grompp (version 4.0.3) output and distances as > calculated by > > > g_traj (version 4.0.3) persist, 2.667 vs. 0.3996 nm. > > > 2. I constructed a three atom system containing 2 reference atoms of > > > type A, and a "pull" atom of type B. Proper output from grompp was > > > observed for all coordinates of both the reference and pulled atoms, > > > include coordinates for atoms moved outside the box in the x-y plane. > > > The coordinate, topology, and run control parameter file are given > below. > > > > > > If there are additional suggestions, I would be greatly appreciative. > > > > > > Thank you, > > > > > > Steve Fiedler > > > > > > ----------------- > > > conf.gro > > > Three atoms > > > 3 > > > 1AAA A 1 1.500 1.500 1.000 > > > 2AAA A 2 0.500 1.500 1.000 > > > 3BBB B 3 -1.500 1.500 1.700 > > > 3.00000 3.00000 3.00000 > > > ----------------- > > > index.ndx > > > [ System ] > > > 1 2 3 > > > [ Ref ] > > > 1 2 > > > [ Pulled ] > > > 3 > > > ----------------- > > > grompp.mdp > > > title = ThreeAtoms > > > integrator = md > > > dt = 0.001 > > > nsteps = 1 > > > ns_type = grid > > > pbc = xyz > > > coulombtype = shift > > > rlist = 1.4 > > > rcoulomb = 1.4 > > > rvdw = 1.4 > > > tcoupl = no > > > pcoupl = no > > > constraint_algorithm = shake > > > shake_tol = 1e-4 > > > gen-vel = no > > > gen-temp = 0 > > > > > > nstxout = 1 > > > nstvout = 0 > > > nstfout = 0 > > > > > > pull = umbrella > > > pull_geometry = distance > > > pull_dim = N N Y > > > pull_start = no > > > pull_init1 = 0.7 > > > pull_group0 = Ref > > > pull_group1 = Pulled > > > pull_k1 = 10000 > > > ----------------- > > > topology.top > > > ; topology for two partially charged atoms > > > > > > [ defaults ] > > > ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ > > > 1 3 yes 0.125 0.5 > > > > > > [ atomtypes ] > > > ;name mass charge ptype sig eps > > > A 1000.0000 0.000 A 0.50000 9.90000 > > > B 9.0000 0.000 A 0.30000 9.00000 > > > > > > [ nonbond_params ] > > > ; i j func sig eps > > > > > > [ moleculetype ] > > > AAAA 1 > > > > > > [ atoms ] > > > ; nr type resnr residue atom cgnr charge mass > > > 1 A 1 AAA A 1 0.000 1000.0000 > > > > > > [ moleculetype ] > > > BBBB 1 > > > > > > [ atoms ] > > > ; nr type resnr residue atom cgnr charge mass > > > 1 B 1 BBB B 1 0.000 9.00 > > > > > > [ system ] > > > ; name > > > Three atoms > > > > > > [ molecules ] > > > ; name number > > > AAAA 2 > > > BBBB 1 > > > > > > > > > > > > > > > > > > Chris Neale wrote: > > >> I just checked similar simulations of mine and Berk's suggestion > > >> accounts for similar discrepancies that I notice on a quick > > >> evaluation where g_traj and g_dist fail to give me the same distance > > >> as I obtain from the pull pos.xvg file. As Berk suggests, once I > > >> first trjconv -center -pbc mol -ur compact (giving an appropriate > > >> residue for centering that puts all relevant pulled atoms in the > same > > >> box) then g_traj and g_dist both give me the exact same answer as I > > >> calculate based on pull pos.xvg. Chris -- original message -- Hi, > > >> There could be a problem with periodic boundary conditions. Do you > > >> have multiple molecules in a pull group, or broken molecules? In > that > > >> case the COM position of 3.3.3 and g_traj are both incorrect. The > > >> pull code in 4.0 grompp and mdrun are (as far as I know) always > > >> correct. Berk > > > > > > _______________________________________________ > > > gmx-users mailing list gmx-users@gromacs.org > > > http://www.gromacs.org/mailman/listinfo/gmx-users > > > Please search the archive at http://www.gromacs.org/search before > > > posting! > > > Please don't post (un)subscribe requests to the list. Use thewww > > > interface or send it to gmx-users-requ...@gromacs.org. > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > > > > > > > -- > > Steve Fiedler, Ph.D. > > Research Fellow > > Department of Mechanical Engineering > > The University of Michigan > > 2024 G.G. Brown > > 2350 Hayward St. > > Ann Arbor, MI 48109-2125 > > > > > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before > posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > ------------------------------------------------------------------------ > What can you do with the new Windows Live? Find out > <http://www.microsoft.com/windows/windowslive/default.aspx> > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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