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 -- 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.
