ok -- thanks -- am to trying this out now. btw, I am also running 2016.3 to analyze a trajectory made with 2016.4. I tried a couple of versions and still got the same weird behavior, but I thought I'd let you know in case you know that using a slightly older version to analyze a newer one is problematic.
M On Fri, Feb 8, 2019 at 8:32 AM Justin Lemkul <jalem...@vt.edu> wrote: > > > On 2/8/19 8:29 AM, Mala L Radhakrishnan wrote: > > Hi Justin, > > > > Yes, but I don't want anything sticking out of the box. I need the shape > > of my entire system, when visualized, to be wholly contained within the > > cubic shape -- and centered on the desired group. That's pretty much > all. > > Does this clarify? Does this change what you recommend? > > Use -pbc atom instead of -pbc mol in my first suggested command. > > -Justin > > > Mala > > > > On Fri, Feb 8, 2019 at 8:18 AM Justin Lemkul <jalem...@vt.edu> wrote: > > > >> > >> On 2/8/19 8:15 AM, Mala L Radhakrishnan wrote: > >>> Hi Justin, > >>> > >>> Also -- this is important, I need to maintain the shape of the cubic > box, > >>> so I do *not* want to keep molecules at the box edges whole (I know > this > >>> sounds weird, but I need it for my applications) -- so should I use > -pbc > >>> atom instead of -pbc mol for the first step? > >> The shape of the box will not change with any of the -pbc options, you > >> may just have a few atoms sticking "out" of the actual dimensions > >> depending on PBC treatment. But the *box* never changes unless you > >> re-wrap or manipulate it with -ur (though, as I've said for a cube, you > >> can't really actually change). > >> > >> -Justin > >> > >>> Thanks again so much -- just want to make sure before I start making > >> these > >>> huge files :) > >>> > >>> Mala > >>> > >>> On Fri, Feb 8, 2019 at 8:07 AM Justin Lemkul <jalem...@vt.edu> wrote: > >>> > >>>> On 2/8/19 8:03 AM, Mala L Radhakrishnan wrote: > >>>>> Hi Justin, > >>>>> > >>>>> Thank you SO much -- I will try this out, but I have a silly question > >>>>> before I do -- is there a way to dump just the desired frame in the > >> first > >>>>> step itself -- or would that screw up the ordering -- since my xtc > >> files > >>>>> are just so huge and I'd rather not create more huge files than > >>>> necessary? > >>>>> If there is no other way, then I will do it, but these are massive > >> files > >>>>> and I'd need to create them for many simulations. > >>>> You can try, but my suggestion is that you have to be careful in > making > >>>> leaps from one reference state to a final state. In principle, it > should > >>>> work no matter what, but I've noticed that trjconv does sometimes > >>>> require processing of a full trajectory for PBC and fitting purposes. > I > >>>> have no explanation as to why, but if you carefully and methodically > >>>> invoke trjconv, there should never be a problem getting it to behave > as > >>>> you need it to. > >>>> > >>>> -Justin > >>>> > >>>>> Thanks, > >>>>> > >>>>> M > >>>>> > >>>>> On Fri, Feb 8, 2019 at 6:56 AM Justin Lemkul <jalem...@vt.edu> > wrote: > >>>>> > >>>>>> On 2/8/19 6:52 AM, Mala L Radhakrishnan wrote: > >>>>>>> Hi Paul, > >>>>>>> > >>>>>>> Thanks for this idea -- > >>>>>>> > >>>>>>> ...But it returns what I would expect: > >>>>>>> > >>>>>>> Statistics over 1 steps [ 200000.0000 through 200000.0000 ps ], 3 > >> data > >>>>>> sets > >>>>>>> All statistics are over 1 points > >>>>>>> > >>>>>>> Energy Average Err.Est. RMSD > Tot-Drift > >>>>>>> > >> > ------------------------------------------------------------------------------- > >>>>>>> Box-X 12.2482 -- 0 > 0 > >>>>>> (nm) > >>>>>>> Box-Y 12.2482 -- 0 > 0 > >>>>>> (nm) > >>>>>>> Box-Z 12.2482 -- 0 > 0 > >>>>>> (nm) > >>>>>>> This matches what the pdb extracted file says (i.e. the file which > >> does > >>>>>> not > >>>>>>> have the complex centered at the Box-X/2, Box-Y/x, Box-Z/2) > >>>>>>> So I'm still not sure what's going on -- any other thoughts? > >>>>>> From your trjconv command, it looks like you are somewhat > >>>> inefficiently > >>>>>> trying to simply output the final frame, is that correct? > >>>>>> > >>>>>> I have found quirky behavior in trjconv when trying to do multiple > >>>>>> actions (you're centering and manipulating PBC at the same time) > while > >>>>>> also skipping many frames. Here's what I would suggest: > >>>>>> > >>>>>> gmx trjconv -s md.tpr -f md.xtc -pbc mol -o md_mol.xtc > >>>>>> gmx trjconv -s md.tpr -f md_mol.xtc -center -o md_center.xtc -n > >>>> index.ndx > >>>>>> gmx trjconv -s md.tpr -f md_center.xtc -dump 200000 > >>>>>> > >>>>>> Does that improve the situation? If not, please send a minimal test > >> case > >>>>>> to me off-list and I will take a look. > >>>>>> > >>>>>> -Justin > >>>>>> > >>>>>>> Mala > >>>>>>> > >>>>>>> > >>>>>>> > >>>>>>> On Fri, Feb 8, 2019 at 5:39 AM Peter Kroon <p.c.kr...@rug.nl> > wrote: > >>>>>>> > >>>>>>>> What does "gmx energy -b 20000 -e 20000" give as box dimensions? > >>>>>>>> > >>>>>>>> > >>>>>>>> Peter > >>>>>>>> > >>>>>>>> On 07-02-19 22:20, Mala L Radhakrishnan wrote: > >>>>>>>>> Hi Justin, > >>>>>>>>> > >>>>>>>>> Thank you -- the good news is that the center of mass of this > group > >>>>>> does > >>>>>>>> in > >>>>>>>>> fact match what I calculate to be the COM with my script. > >>>>>>>>> > >>>>>>>>> BUT, the bad news is that this is not in the center of the box > >> after > >>>> I > >>>>>>>> have > >>>>>>>>> asked for it to be centered (which I presume it should be):: > >>>>>>>>> > >>>>>>>>> COM: > >>>>>>>>> 5.95324 6.00572 5.68943 > >>>>>>>>> > >>>>>>>>> The cubic box is 12.249 long (as noted in the CRYST1 field of the > >> pdb > >>>>>>>> file > >>>>>>>>> and its left corner is at the origin (I know this because I have > >>>> atoms > >>>>>>>> that > >>>>>>>>> go all the way to the edges of the box and my minimum x,y, and x > >>>>>>>>> coordinates are basically 0 and my maximum are basically 12.24 in > >> all > >>>>>>>> three > >>>>>>>>> directions, which would make the center of the box: > >>>>>>>>> > >>>>>>>>> 6.1245, 6.1245, 6.1245 > >>>>>>>>> > >>>>>>>>> So it's close but a few angstroms off. Can you please tell me > what > >>>>>> might > >>>>>>>>> be going on here? I am happy to share files with, as I'd be > really > >>>>>>>>> grateful for your help. Again, I've written a scrip to translate > >> and > >>>>>>>>> "wrap" the atoms across the pbc in the worst case scenario, but I > >>>> have > >>>>>> to > >>>>>>>>> imagine gromacs should be able to do this correctly. > >>>>>>>>> > >>>>>>>>> Again - this is the command I used to extract the hopefully > >> centered > >>>>>>>> frame: > >>>>>>>>> gmx trjconv -f md.xtc -o all.pdb -s md.tpr -b 200000 -e 200000 -n > >>>>>>>> INDEX.ndx > >>>>>>>>> -pbc atom -center > >>>>>>>>> > >>>>>>>>> ...and I chose the correct index (and extracted the same atoms > just > >>>> in > >>>>>>>> case > >>>>>>>>> to make sure that I knew exactly what atoms it thought it was > >>>>>> centering, > >>>>>>>> in > >>>>>>>>> case something was in fact wrong with the index file) > >>>>>>>>> > >>>>>>>>> Thank you so much, > >>>>>>>>> > >>>>>>>>> Mala > >>>>>>>>> > >>>>>>>>> > >>>>>>>>> On Thu, Feb 7, 2019 at 1:54 PM Justin Lemkul <jalem...@vt.edu> > >>>> wrote: > >>>>>>>>>> On 2/7/19 1:52 PM, Mala L Radhakrishnan wrote: > >>>>>>>>>>> Hi Justin, > >>>>>>>>>>> > >>>>>>>>>>> I've verified the I'm entering in the right group and that it's > >>>>>> correct > >>>>>>>>>> in > >>>>>>>>>>> the index file. Where do I find the output for what it thinks > is > >>>> the > >>>>>>>>>>> center of mass before and after? That would be helpful output, > >>>> but I > >>>>>>>>>>> haven't found such output in standard output or error. > >>>>>>>>>> gmx traj -ox -com > >>>>>>>>>> > >>>>>>>>>> -Justin > >>>>>>>>>> > >>>>>>>>>>> thanks again for instructions on how to get this info.. > >>>>>>>>>>> Mala > >>>>>>>>>>> > >>>>>>>>>>> On Thu, Feb 7, 2019 at 1:46 PM Justin Lemkul <jalem...@vt.edu> > >>>>>> wrote: > >>>>>>>>>>>> On 2/7/19 1:36 PM, Mala L Radhakrishnan wrote: > >>>>>>>>>>>>> Thanks...but these don't really address the issue I have. > I've > >>>>>>>> written > >>>>>>>>>>>> my > >>>>>>>>>>>>> own script now to do re-centering and looping of atoms across > >> the > >>>>>> box > >>>>>>>>>>>> walls > >>>>>>>>>>>>> myself, but I am still really unclear why -center does not in > >>>> fact > >>>>>>>>>> center > >>>>>>>>>>>>> the molecule in the box either at its geometric center OR its > >>>>>> center > >>>>>>>> of > >>>>>>>>>>>>> mass (I have written scripts to test both out and neither > >> match, > >>>>>> and > >>>>>>>>>>>>> visually the molecule is clearly not centered in the box) > >>>>>>>>>>>>> > >>>>>>>>>>>>> To me it definitely seems like something is not right with > this > >>>>>>>> utility > >>>>>>>>>>>> or > >>>>>>>>>>>>> something about the options I've used are conflicting in > ways I > >>>>>> don't > >>>>>>>>>>>>> understand: > >>>>>>>>>>>>> -pbc atom -center (a group from index file) > >>>>>>>>>>>>> > >>>>>>>>>>>>> Thanks again for any other ideas... > >>>>>>>>>>>> I've only been loosely following this thread, but I've never > >> had a > >>>>>>>>>>>> problem where trjconv didn't center as I wanted. Have you > >> verified > >>>>>>>> that > >>>>>>>>>>>> the index group is correct, and you're making the proper > >>>> selection? > >>>>>>>> What > >>>>>>>>>>>> does gmx traj report as the center-of-mass coordinates for > those > >>>>>>>> groups > >>>>>>>>>>>> before and after trjconv tries to center them? > >>>>>>>>>>>> > >>>>>>>>>>>> -Justin > >>>>>>>>>>>> > >>>>>>>>>>>> -- > >>>>>>>>>>>> ================================================== > >>>>>>>>>>>> > >>>>>>>>>>>> Justin A. Lemkul, Ph.D. > >>>>>>>>>>>> Assistant Professor > >>>>>>>>>>>> Office: 301 Fralin Hall > >>>>>>>>>>>> Lab: 303 Engel Hall > >>>>>>>>>>>> > >>>>>>>>>>>> Virginia Tech Department of Biochemistry > >>>>>>>>>>>> 340 West Campus Dr. > >>>>>>>>>>>> Blacksburg, VA 24061 > >>>>>>>>>>>> > >>>>>>>>>>>> jalem...@vt.edu | (540) 231-3129 > >>>>>>>>>>>> http://www.thelemkullab.com > >>>>>>>>>>>> > >>>>>>>>>>>> ================================================== > >>>>>>>>>>>> > >>>>>>>>>>>> -- > >>>>>>>>>>>> Gromacs Users mailing list > >>>>>>>>>>>> > >>>>>>>>>>>> * Please search the archive at > >>>>>>>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List > >>>> before > >>>>>>>>>>>> posting! > >>>>>>>>>>>> > >>>>>>>>>>>> * Can't post? Read > http://www.gromacs.org/Support/Mailing_Lists > >>>>>>>>>>>> > >>>>>>>>>>>> * For (un)subscribe requests visit > >>>>>>>>>>>> > >>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > >>>>>> or > >>>>>>>>>>>> send a mail to gmx-users-requ...@gromacs.org. > >>>>>>>>>>>> > >>>>>>>>>> -- > >>>>>>>>>> ================================================== > >>>>>>>>>> > >>>>>>>>>> Justin A. Lemkul, Ph.D. > >>>>>>>>>> Assistant Professor > >>>>>>>>>> Office: 301 Fralin Hall > >>>>>>>>>> Lab: 303 Engel Hall > >>>>>>>>>> > >>>>>>>>>> Virginia Tech Department of Biochemistry > >>>>>>>>>> 340 West Campus Dr. > >>>>>>>>>> Blacksburg, VA 24061 > >>>>>>>>>> > >>>>>>>>>> jalem...@vt.edu | (540) 231-3129 > >>>>>>>>>> http://www.thelemkullab.com > >>>>>>>>>> > >>>>>>>>>> ================================================== > >>>>>>>>>> > >>>>>>>>>> -- > >>>>>>>>>> Gromacs Users mailing list > >>>>>>>>>> > >>>>>>>>>> * Please search the archive at > >>>>>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List > >> before > >>>>>>>>>> posting! > >>>>>>>>>> > >>>>>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >>>>>>>>>> > >>>>>>>>>> * For (un)subscribe requests visit > >>>>>>>>>> > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > >>>> or > >>>>>>>>>> send a mail to gmx-users-requ...@gromacs.org. > >>>>>>>>>> > >>>>>>>> -- > >>>>>>>> Gromacs Users mailing list > >>>>>>>> > >>>>>>>> * Please search the archive at > >>>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List > before > >>>>>>>> posting! > >>>>>>>> > >>>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >>>>>>>> > >>>>>>>> * For (un)subscribe requests visit > >>>>>>>> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > >> or > >>>>>>>> send a mail to gmx-users-requ...@gromacs.org. > >>>>>>>> > >>>>>> -- > >>>>>> ================================================== > >>>>>> > >>>>>> Justin A. Lemkul, Ph.D. > >>>>>> Assistant Professor > >>>>>> Office: 301 Fralin Hall > >>>>>> Lab: 303 Engel Hall > >>>>>> > >>>>>> Virginia Tech Department of Biochemistry > >>>>>> 340 West Campus Dr. > >>>>>> Blacksburg, VA 24061 > >>>>>> > >>>>>> jalem...@vt.edu | (540) 231-3129 > >>>>>> http://www.thelemkullab.com > >>>>>> > >>>>>> ================================================== > >>>>>> > >>>>>> -- > >>>>>> Gromacs Users mailing list > >>>>>> > >>>>>> * Please search the archive at > >>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >>>>>> posting! > >>>>>> > >>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >>>>>> > >>>>>> * For (un)subscribe requests visit > >>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or > >>>>>> send a mail to gmx-users-requ...@gromacs.org. > >>>>>> > >>>> -- > >>>> ================================================== > >>>> > >>>> Justin A. Lemkul, Ph.D. > >>>> Assistant Professor > >>>> Office: 301 Fralin Hall > >>>> Lab: 303 Engel Hall > >>>> > >>>> Virginia Tech Department of Biochemistry > >>>> 340 West Campus Dr. > >>>> Blacksburg, VA 24061 > >>>> > >>>> jalem...@vt.edu | (540) 231-3129 > >>>> http://www.thelemkullab.com > >>>> > >>>> ================================================== > >>>> > >>>> -- > >>>> Gromacs Users mailing list > >>>> > >>>> * Please search the archive at > >>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >>>> posting! > >>>> > >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >>>> > >>>> * For (un)subscribe requests visit > >>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >>>> send a mail to gmx-users-requ...@gromacs.org. > >>>> > >> -- > >> ================================================== > >> > >> Justin A. Lemkul, Ph.D. > >> Assistant Professor > >> Office: 301 Fralin Hall > >> Lab: 303 Engel Hall > >> > >> Virginia Tech Department of Biochemistry > >> 340 West Campus Dr. > >> Blacksburg, VA 24061 > >> > >> jalem...@vt.edu | (540) 231-3129 > >> http://www.thelemkullab.com > >> > >> ================================================== > >> > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-requ...@gromacs.org. > >> > > > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Mala L. Radhakrishnan Whitehead Associate Professor of Critical Thought Associate Professor of Chemistry Wellesley College 106 Central Street Wellesley, MA 02481 (781)283-2981 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.