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 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 11:58 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using Hey Vito, Can you paste your exact workflow? Cheers, Tsjerk On Wed, May 21, 2014 at 9:53 AM, Vito Genna <vito.ge...@iit.it> wrote: > Hi Tsierk, > > Hi tried your protocol without success. > I have also tried different centering combination (on > protein/DNA/Ligand/Protein+DNA/DNA+Ligand/Protein+ligand) > and different flags combo (-pbc mol -ur compact/rect). > I have added also the pbc whole before -pbc nojump but the result at the > end is always the same, as shown in fig > http://wikisend.com/download/185858/fig5.png > The bonds are disappeared it's a god start but it is not enough to make > measurements inside the catalytic pocket. > > I hope to find a solution with you and to write down a protocol for people > which work whit ternary complexes. > > Thank you for your time. > > Best Regards > > 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: Tuesday, May 20, 2014 9:37 PM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems > for VMD using > > Hi Vito, > > If the .tpr file is good, i.e. has everything assembled the way you want, > then the first step is trjconv -pbc nojump. That will make sure that > nothing gets split over PBC. Then center the protein in the box (trjconv > -center), and subsequently put all molecules in the box (-pbc mol -ur > compact/rect). > > Cheers, > > Tsjerk > > > > On Tue, May 20, 2014 at 7:51 PM, Vito Genna <vito.ge...@iit.it> wrote: > > > Hi Tsjerk, > > > > Thank you for your email. > > No it is not broken. The structure is intact till the 20 ns of production > > phase. > > I have already used the .tpr (both md_0_1.tpr before, and then npt.tpr) > > obtaining the same result. > > Basically you are suggesting to fix the first frame of the production > > phase and use it as a reference point > > for the subsequent manipulations (-pbs nojump) of all TRJs? > > I'm going to do this attempt and I will keep you posted. > > > > Thanks again. > > > > 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 Tsjerk > > Wassenaar [tsje...@gmail.com] > > Sent: Tuesday, May 20, 2014 7:30 PM > > To: Discussion list for GROMACS users > > Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems > > for VMD using > > > > Hi Vito, > > > > Was the structure already broken up when you solvated it? If not, which > > seems likely to me, then you can use that structure, or the .tpr from the > > EM in solvent, to remove jumps from the first frame of your run. After > you > > unbroke the first frame, you can use that as reference for processing > your > > trajectory with -pbc nojump. > > > > Hope it helps, > > > > Tsjerk > > > > > > On Tue, May 20, 2014 at 7:14 PM, Vito Genna <vito.ge...@iit.it> wrote: > > > > > Dear Justin, > > > > > > Thank you for your email. > > > As in your case, my system is formed by a Protein + dsDNA + structural > > > ions + counterions + ligand + water > > > I guess that I have too much element to efficiently solve the problem > but > > > I want to try to fix it. The solution could help > > > other people to avoid to became crazy with this kind of TRJs > > manipulations. > > > > > > Figs. link: http://wikisend.com/download/571570/pics.zip > > > > > > Well. today I tried a different combo as: > > > > > > A) trjconv -s -f -pbc mol(res) -center (-n index with > > > DNA&Protein/Ligand/Protein) > > > > > > to obtain trajectories as shown in pic1 > > > > > > B) Then i used -pbc whole/nojump to obtain a result as shown in fig 2 > > > > > > I guess that the problem still persists.... > > > > > > Any suggestion about your experience? > > > > > > Thanks in advance > > > > > > 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 Justin > > > Lemkul [jalem...@vt.edu] > > > Sent: Monday, May 19, 2014 11:26 PM > > > To: gmx-us...@gromacs.org > > > Subject: Re: [gmx-users] How to efficiently fix pbc trajectories > problems > > > for VMD using > > > > > > On 5/19/14, 12:29 PM, Vito Genna wrote: > > > > Dear Mark, > > > > > > > > You can see the results of -pbc whole and -pbc nojump on this pics > > > http://wikisend.com/download/777550/PICs.zip > > > > I tried to use the flag -s with the .tpr and then with the .gro file > > but > > > in both cases I obtain a result similar to that one shown on > > > > PICs on link. A broken system. > > > > Both .tpr and .gro used for the -pbc whole/nojumo/fit are ok and the > > > system is complete.During the equillibration and for the first ~20ns of > > > production phase > > > > the system is stable within the box. The problem start to appear as > > soon > > > as the system leaves the first box (~25ns) > > > > > > > > > > Can you post an image looking straight-on at the system, with box > vectors > > > rendered, with and without water? The oblique shots you've provided > are > > a > > > bit > > > hard to interpret. > > > > > > I've dealt with very complex systems like these (multiple proteins + > > dsDNA > > > + > > > ions + ligands) and it is a pain. I believe I went through 6 rounds of > > > trjconv > > > for most of them (hundreds of ns in length). The exact protocol is > > highly > > > system-specific, but the key is that it is often necessary to use > custom > > > index > > > groups (a specific residue, or a few in some key location) for > centering > > > and/or > > > fitting. > > > > > > -Justin > > > > > > > Thanks in advance > > > > > > > > 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 Mark > > > Abraham [mark.j.abra...@gmail.com] > > > > Sent: Monday, May 19, 2014 5:32 PM > > > > To: Discussion list for GROMACS users > > > > Subject: Re: [gmx-users] How to efficiently fix pbc trajectories > > > problems for VMD using > > > > > > > > On Mon, May 19, 2014 at 5:03 PM, Vito Genna <vito.ge...@iit.it> > wrote: > > > > > > > >> Dear Mark, > > > >> > > > >> Thank you for you prompt reply. > > > >> Yes, indeed I was following the suggested trjconv workflow. Right > you > > > are. > > > >> When I say "does not work" I mean that the system is stretched > between > > > two > > > >> adjacent boxes showing internal bonds that run throughout the "main" > > pbc > > > >> box (extremely long). > > > >> > > > >> Regarding the steps: > > > >> Yes I already visualized the results step by step and after the 1) > one > > > >> trjconv fixes the bond problems but splits my protein in two > distinct > > > part > > > >> (the protein contains only 1 chain) moving them in two boxes. > > > >> > > > > > > > > Sounds like you mean trjconv from your 1)a). Please be specific. If > so, > > > > IIRC, -pbc whole restores the "wholeness" as it judges from state of > > the > > > -s > > > > input. So if you made the .tpr from a .gro file that had the protein > in > > > two > > > > chunks across periodic boundaries from the equilibration, so will the > > > > output be split. This was what I guessed before, but you didn't > report > > > > whether you investigated whether your .tpr file contained what you > > think > > > it > > > > does. IIRC you can also use a coordinate file for -s for that stage, > > > since > > > > "-pbc whole" does not actually use the topology, and it is easier to > > > > construct a .gro file that looks how you want. > > > > > > > > Mark > > > > > > > > At this point I use the -pbc nojump option that gives me the same > > > previous > > > >> problem (bond excessively long). > > > >> > > > >> If I could reassembly the protein after -pbc whole action I'll be > > > >> completely satisfied. > > > >> > > > >> Any suggestion? > > > >> > > > >> Thank in advance. > > > >> > > > >> Cheers > > > >> > > > >> 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 > Mark > > > >> Abraham [mark.j.abra...@gmail.com] > > > >> Sent: Monday, May 19, 2014 4:31 PM > > > >> To: Discussion list for GROMACS users > > > >> Subject: Re: [gmx-users] How to efficiently fix pbc trajectories > > > problems > > > >> for VMD using > > > >> > > > >> You seem to be following > > > >> > > > >> > > > > > > http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions > > > >> , > > > >> which is good. But it's hard to help when we don't know what you > think > > > >> "doesn't work" means. Make sure that the things you think are whole > in > > > >> md_0_1.tpr actually are. Visualize your intermediate stages of 1) to > > see > > > >> where the issue arises. If you need to, upload some pictures to a > file > > > >> sharing service that show what the input and unsatisfactory output > > was. > > > >> > > > >> Mark > > > >> > > > >> On Mon, May 19, 2014 at 3:15 PM, Vito Genna <vito.ge...@iit.it> > > wrote: > > > >> > > > >>> Hi to everybody, > > > >>> > > > >>> My name is Vito and I would like to share with you (and discuss > also) > > > the > > > >>> problems that I have found during my TRJs analysis. > > > >>> I have a system made by: Protein + dsDNA + Ligand. I obtained my > > single > > > >>> precision trajectory in a .xtc file. > > > >>> Well, I'd like to analyze my TRJs using VMD due to its intrinsic > > > velocity > > > >>> in calcuating (Distances, angles, RMSD and so on) but I cannot do > it > > > >>> because I encounter a serious issue with the visualization (pbc > > > problems > > > >> as > > > >>> you surely know) > > > >>> To try to avoid the problem I've used several protocols, without > > > success: > > > >>> > > > >>> 1) > > > >>> > > > >>> a) trjconv_mpi -f md_0_1.part0001.xtc -o md_0_1-whole.xtc -s > > md_0_1.tpr > > > >>> -pbc whole (on the entire system) > > > >>> b) trjconv_mpi -f md_0_1-whole.xtc -o md_0_1-nojump.xtc -s > md_0_1.tpr > > > >> -pbc > > > >>> nojump > > > >>> (on the entire system) > > > >>> c) trjconv_mpi -f md_0_1-nojump.xtc -o md_0_1-fit.xtc -s md_0_1.tpr > > > -fit > > > >>> progressive (on Protein only) > > > >>> > > > >>> It does not work. > > > >>> > > > >>> 2) > > > >>> > > > >>> a) trjconv_mpi -f (as the previous one) -pbc mol -ur compact > -center > > -o > > > >>> compact.xtc > > > >>> > > > >>> It does not work as well. > > > >>> > > > >>> 3) Option 2 changing the flag -pbc mol with -pbc res > > > >>> > > > >>> It does not work. > > > >>> > > > >>> New idea? New possible combo? > > > >>> > > > >>> Thanks in advance for your replies. > > > >>> > > > >>> All the best > > > >>> > > > >>> Vito > > > >>> > > > >>> > > > >>> > > > >>> > > > >>> 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 > > > >>> > > > >>> -- > > > >>> 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-usersor > > > >>> 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-usersor > > > >> 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-usersor > > > >> 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-usersor > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > > > > > -- > > > ================================================== > > > > > > Justin A. Lemkul, Ph.D. > > > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > > > > > Department of Pharmaceutical Sciences > > > School of Pharmacy > > > Health Sciences Facility II, Room 601 > > > University of Maryland, Baltimore > > > 20 Penn St. > > > Baltimore, MD 21201 > > > > > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > > http://mackerell.umaryland.edu/~jalemkul > > > > > > ================================================== > > > -- > > > 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. > > -- > > 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. > -- > 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. -- 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.