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)
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-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. -- 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.