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 <[email protected]> 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: [email protected] [ > [email protected]] on behalf of Tsjerk > Wassenaar [[email protected]] > 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 <[email protected]> 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: [email protected] [ > > [email protected]] on behalf of Justin > > Lemkul [[email protected]] > > Sent: Monday, May 19, 2014 11:26 PM > > To: [email protected] > > 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: [email protected] [ > > [email protected]] on behalf of Mark > > Abraham [[email protected]] > > > 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 <[email protected]> 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: [email protected] [ > > >> [email protected]] on behalf of Mark > > >> Abraham [[email protected]] > > >> 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 <[email protected]> > 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 [email protected]. > > >>> > > >> -- > > >> 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 [email protected]. > > >> -- > > >> 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 [email protected]. > > >> > > > -- > > > 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 [email protected]. > > > > > > > -- > > ================================================== > > > > 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 > > > > [email protected] | (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 [email protected]. > > -- > > 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 [email protected]. > > > > > > -- > 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 [email protected]. > -- > 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 [email protected]. > -- 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 [email protected].
