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?
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. > -- 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.
