...and molecules at the edges can totally be broken. So really just a translation of the box coordinates to be centered on the desired group. It should really be very straighforward.
If it's easier to take offline, I'm happy to. M On Fri, Feb 8, 2019 at 8:29 AM Mala L Radhakrishnan <mradh...@wellesley.edu> 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? > > 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. >> > > > -- > Mala L. Radhakrishnan > Whitehead Associate Professor of Critical Thought > Associate Professor of Chemistry > Wellesley College > 106 Central Street > Wellesley, MA 02481 > (781)283-2981 > -- 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.
