Hi Vito, Does npt.tpr correspond to the first frame of the trajectory and is the structure in npt.tpr correctly assembled? (editconf -f npt.tpr -o npt.tpr.pdb, and check). The only way that -pbc nojump can give a final frame in which the complex is separated is if the reference structure has them already separated. In that case, nothing you'll try will give you what you want. What I do in such cases is dump the first frame, using -pbc whole, and then shift the chains in Pymol according to the box vectors to have them together. Then I use the resulting structure as reference for processing the trajectory.
Cheers, Tsjerk On Thu, May 22, 2014 at 10:59 AM, Vito Genna <vito.ge...@iit.it> wrote: > Dear Dr. Warrem, Dear Tsjerk, > > Thank you for your emails. > Following the suggestion of Dr. Warren I created several dir in which I > applied different protocols on my system > > -- DIR1 -- > > 1) trjconv_mpi -s npt.tpr -f test.xtc -o test-nojump.xtc -pbc nojump > (output System) > > 2) trjconv_mpi -s npt.tpr -f test-nojump.xtc -o test-center.xtc - center > -n iindex.ndx (centering all the frames on Protein) (output system) > > 3) trjconv_mpi -s npt.tpr -f test-center.xtc -o test-compact.xtc -pbc mol > -ur rect (output System) > > The related Figures are in the following link: > http://wikisend.com/download/832038/Figtest1.zip > > #Comment: I obtain the same result also if a change rect with compact in > the third step. > > -- DIR2 -- > > 1) trjconv_mpi -s npt.tpr -f test.xtc -o test-nojump.xtc -pbc nojump > (output System) > > 2) trjconv_mpi -s npt.tpr -f test-nojump.xtc -o test-center.xtc - center > -n iindex.ndx (centering all the frames on Protein) (output system) > > 3) trjconv_mpi -s npt.tpr -f test-center.xtc -o test-compact.xtc -pbc mol > -ur rect (output System) > > 4) trjconv_mpi -s npt.tpr -f test-compact.xtc -o test-fit.xtc -fit > progressive (fitting on Protein) > > The pics are here: http://wikisend.com/download/615140/FigTest2.zip > > #Comment: Here again, I obtain the same results as in the DIR1 but My > protein has not translational motions. > #Comment: In the step 2 i also centered the system on the Protein_DNA, > nothing changes. > > > Then, I tried different pbc/centering combination again but I strongly > believe that fixing DNA-Protein complex is enough to obtain a good system. > > What would do you do to bring back the dsDNA inside the protein? > In which step would you operate your command? > > Thanks in advance for your time. > > Cheers > > > V > > > > > Vito Genna, PhD-Fellow > Italian Institute of Technology > Drug Discovery and Development department > Via Morego 30, 16163 Genoa, Italy > > > ------------------------------------------------------------------------------------------------------------- > The process of scientific discovery is, in effect, a continual flight from > wonder. > Albert Einstein > > > ________________________________________ > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [ > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Dallas > Warren [dallas.war...@monash.edu] > Sent: Thursday, May 22, 2014 1:40 AM > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems > for VMD using > > Would suggest that each time you try a different workflow, do so in a new > subdirectory and copy the required files into there. That way you ensure > are using the files you think that you are. > > Will help those assisting to then post an image of the coordinate files at > each step of the work flow, to see how things are changing, or not. > > Catch ya, > > Dr. Dallas Warren > Drug Delivery, Disposition and Dynamics > Monash Institute of Pharmaceutical Sciences, Monash University > 381 Royal Parade, Parkville VIC 3052 > dallas.war...@monash.edu > +61 3 9903 9304 > --------------------------------- > When the only tool you own is a hammer, every problem begins to resemble a > nail. > > > -----Original Message----- > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > > [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of > > Vito Genna > > Sent: Wednesday, 21 May 2014 11:07 PM > > To: gmx-us...@gromacs.org > > Subject: Re: [gmx-users] How to efficiently fix pbc trajectories > > problems for VMD using > > > > Dear Tsjerk, > > > > No, it doesn't. (http://wikisend.com/download/324888/Post-nojump.png) > > I think that the first step need to be changed that's why I tried (whit > > no success) > > the flag -pbc whole. I'm still looking for a solution. > > > > Thanks again. > > > > V > > > > Vito Genna, PhD-Fellow > > Italian Institute of Technology > > Drug Discovery and Development department > > Via Morego 30, 16163 Genoa, Italy > > > > ----------------------------------------------------------------------- > > -------------------------------------- > > The process of scientific discovery is, in effect, a continual flight > > from wonder. > > Albert Einstein > > > > > > ________________________________________ > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > > [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Tsjerk > > Wassenaar [tsje...@gmail.com] > > Sent: Wednesday, May 21, 2014 1:48 PM > > To: Discussion list for GROMACS users > > Subject: Re: [gmx-users] How to efficiently fix pbc trajectories > > problems for VMD using > > > > Hey Vito, > > > > After the first step, does the trajectory (say the last frame) look > > fine? > > If it does (everything nicely assembled), then after the second step, > > does > > it still look fine, and is it placed properly in the center of the box? > > > > Cheers, > > > > Tsjerk > > > > > > On Wed, May 21, 2014 at 12:50 PM, Vito Genna <vito.ge...@iit.it> wrote: > > > > > Hi Tsierk, > > > > > > Ok. > > > > > > 1) trjconv_mpi -s em.tpr -f test.xtc -o test-nojump.xtc -pbc nojump > > > (output System) > > > > > > 2) trjconv_mpi -s em.tpr -f test-nojump.xtc -o test-center.xtc - > > center -n > > > index.ndx (centering all the frames on different targets Protein/DNA > > ecc > > > ecc) (output system) > > > > > > 3) trjconv_mpi -s em.tpr -f test-center.xtc -o test-compact.xtc -pbc > > mol > > > -ur rect[or compact] (output System) > > > > > > I also tried, successively, the same procedure adding one step more: > > -pbc > > > whole > > > This last step was added before the step 1. > > > > > > But at the end I obtain the same result. > > > > > > Surely, I'm doing something wrong but I'm not understand what is > > wrong...:/ > > > > > > Thank you for your time. > > > > > > V > > > > > > > > -- > > 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. > -- > 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. > -- Tsjerk A. Wassenaar, Ph.D. -- 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.
