Hi there, have look to arrange_objects.tcl in http://people.sissa.it/~xbiarnes/tools.php. That could be useful for your task.
and -----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: lunedì 19 maggio 2014 17:04 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using 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. 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-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.