Re: [gmx-users] -pbc nojump failure
Dear Irem, You may want to run the trajectory through trjconv and translate it, or use e.g. -pbc whole, so that the protein is intact at frame 1. Then you can run trjconv -pbc nojump on the resulting trajectory. This usually requires a bit of trial and error. Kind regards, Erik > On 31 Mar 2016, at 18:36, Irem Altan wrote: > > I think the problem is that I can’t seem to start from an unfragmented > structure. I start from the .pdb file, where the protein is a whole, and end > up with a .tpr file that is fragmented. The interesting thing is, this did > not happen with version 4.6.5 (I now use 5.1.2). Do I have to do something > extra while preparing the simulation system? > > Here is what I’m currently doing: > > gmx pdb2gmx -f .pdb -o box.gro -p topol.top (then I choose > amber99sb and tip4pew) > gmx solvate -cp box.gro -cs tip4p -p topol.top -o box_h2o.gro > gmx grompp -f ions.mdp -c box_h2o.gro -o ions.tpr -p topol.top > gmx genion -s ions.tpr -p topol.top -o ions.gro -neutral -conc 0.05 (I > choose to replace the solvation waters, SOL) > gmx -f minim.mdp -p topol.top -c ions.gro -o em.tpr > gmx mdrun -v -deffnm em > gmx grompp -f nvt.mdp -p topol.top -c em.gro -o nvt_water_frozen.tpr > > Then I run the simulation with mdrun. The .mdp files are almost identical to > Justin’s files from the Lysozyme tutorial. In the above steps, is there > something that seems like it could cause the fragmentation issue? > > Best, > Irem > >> On Mar 31, 2016, at 11:54 AM, Tsjerk Wassenaar wrote: >> >> No! You can't do that, because fitting will cause the PBC and the >> coordinates to mismatch. So 'nojump' after that will for sure screw up the >> coordinates. Check the trjconv workflow on the Gromacs site. >> >> Cheers, >> >> Tsjerk >> On Mar 31, 2016 14:23, "Francesco Carbone" wrote: >> >>> You could try to fit first (-fit rot+trans) and fix pbc (-pbc nojump) >>> later. >>> >>> Cheers, >>> >>> Fra >>> >>> On 31 March 2016 at 05:45, Tsjerk Wassenaar wrote: >>> Hi Irem, Check the structure in nvt_water_frozen.tpr: gmx editconf -f nvt_water_frozen.tpr -o ref.pdb Cheers, Tsjerk On Mar 31, 2016 00:04, "Irem Altan" wrote: > Hi, > > I am simulating a protein in its unit cell. I use the original .pdb >>> file > as an input, so the initial molecule is not fragmented. At the end of >>> the > simulation, I generate a .pdb file containing the trajectory of the protein > as follows: > > gmx trjconv -f nvt_water_frozen.trr -s nvt_water_frozen.tpr -dt 20 -pbc > nojump -o prot.pdb > > Despite the fact that I use -pbc nojump, I still get all the >>> coordinates > wrapped into the unit cell, and therefore the protein fragmented. What > could be wrong? (I use GROMACS 5.1.2) > > Best, > Irem > -- > 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. -- Gromacs Users mailing list * Please search the archive at http://www.
Re: [gmx-users] -pbc nojump failure
I think the problem is that I can’t seem to start from an unfragmented structure. I start from the .pdb file, where the protein is a whole, and end up with a .tpr file that is fragmented. The interesting thing is, this did not happen with version 4.6.5 (I now use 5.1.2). Do I have to do something extra while preparing the simulation system? Here is what I’m currently doing: gmx pdb2gmx -f .pdb -o box.gro -p topol.top (then I choose amber99sb and tip4pew) gmx solvate -cp box.gro -cs tip4p -p topol.top -o box_h2o.gro gmx grompp -f ions.mdp -c box_h2o.gro -o ions.tpr -p topol.top gmx genion -s ions.tpr -p topol.top -o ions.gro -neutral -conc 0.05 (I choose to replace the solvation waters, SOL) gmx -f minim.mdp -p topol.top -c ions.gro -o em.tpr gmx mdrun -v -deffnm em gmx grompp -f nvt.mdp -p topol.top -c em.gro -o nvt_water_frozen.tpr Then I run the simulation with mdrun. The .mdp files are almost identical to Justin’s files from the Lysozyme tutorial. In the above steps, is there something that seems like it could cause the fragmentation issue? Best, Irem > On Mar 31, 2016, at 11:54 AM, Tsjerk Wassenaar wrote: > > No! You can't do that, because fitting will cause the PBC and the > coordinates to mismatch. So 'nojump' after that will for sure screw up the > coordinates. Check the trjconv workflow on the Gromacs site. > > Cheers, > > Tsjerk > On Mar 31, 2016 14:23, "Francesco Carbone" wrote: > >> You could try to fit first (-fit rot+trans) and fix pbc (-pbc nojump) >> later. >> >> Cheers, >> >> Fra >> >> On 31 March 2016 at 05:45, Tsjerk Wassenaar wrote: >> >>> Hi Irem, >>> >>> Check the structure in nvt_water_frozen.tpr: >>> >>> gmx editconf -f nvt_water_frozen.tpr -o ref.pdb >>> >>> Cheers, >>> >>> Tsjerk >>> On Mar 31, 2016 00:04, "Irem Altan" wrote: >>> Hi, I am simulating a protein in its unit cell. I use the original .pdb >> file as an input, so the initial molecule is not fragmented. At the end of >> the simulation, I generate a .pdb file containing the trajectory of the >>> protein as follows: gmx trjconv -f nvt_water_frozen.trr -s nvt_water_frozen.tpr -dt 20 -pbc nojump -o prot.pdb Despite the fact that I use -pbc nojump, I still get all the >> coordinates wrapped into the unit cell, and therefore the protein fragmented. What could be wrong? (I use GROMACS 5.1.2) Best, Irem -- 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.
Re: [gmx-users] -pbc nojump failure
No! You can't do that, because fitting will cause the PBC and the coordinates to mismatch. So 'nojump' after that will for sure screw up the coordinates. Check the trjconv workflow on the Gromacs site. Cheers, Tsjerk On Mar 31, 2016 14:23, "Francesco Carbone" wrote: > You could try to fit first (-fit rot+trans) and fix pbc (-pbc nojump) > later. > > Cheers, > > Fra > > On 31 March 2016 at 05:45, Tsjerk Wassenaar wrote: > > > Hi Irem, > > > > Check the structure in nvt_water_frozen.tpr: > > > > gmx editconf -f nvt_water_frozen.tpr -o ref.pdb > > > > Cheers, > > > > Tsjerk > > On Mar 31, 2016 00:04, "Irem Altan" wrote: > > > > > Hi, > > > > > > I am simulating a protein in its unit cell. I use the original .pdb > file > > > as an input, so the initial molecule is not fragmented. At the end of > the > > > simulation, I generate a .pdb file containing the trajectory of the > > protein > > > as follows: > > > > > > gmx trjconv -f nvt_water_frozen.trr -s nvt_water_frozen.tpr -dt 20 -pbc > > > nojump -o prot.pdb > > > > > > Despite the fact that I use -pbc nojump, I still get all the > coordinates > > > wrapped into the unit cell, and therefore the protein fragmented. What > > > could be wrong? (I use GROMACS 5.1.2) > > > > > > Best, > > > Irem > > > -- > > > 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.
Re: [gmx-users] -pbc nojump failure
Hi, Thanks. If I do that, the reference structure would be what’s in the .tpr file, right? Best, Irem > On Mar 31, 2016, at 8:22 AM, Francesco Carbone wrote: > > You could try to fit first (-fit rot+trans) and fix pbc (-pbc nojump) later. > > Cheers, > > Fra > > On 31 March 2016 at 05:45, Tsjerk Wassenaar wrote: > >> Hi Irem, >> >> Check the structure in nvt_water_frozen.tpr: >> >> gmx editconf -f nvt_water_frozen.tpr -o ref.pdb >> >> Cheers, >> >> Tsjerk >> On Mar 31, 2016 00:04, "Irem Altan" wrote: >> >>> Hi, >>> >>> I am simulating a protein in its unit cell. I use the original .pdb file >>> as an input, so the initial molecule is not fragmented. At the end of the >>> simulation, I generate a .pdb file containing the trajectory of the >> protein >>> as follows: >>> >>> gmx trjconv -f nvt_water_frozen.trr -s nvt_water_frozen.tpr -dt 20 -pbc >>> nojump -o prot.pdb >>> >>> Despite the fact that I use -pbc nojump, I still get all the coordinates >>> wrapped into the unit cell, and therefore the protein fragmented. What >>> could be wrong? (I use GROMACS 5.1.2) >>> >>> Best, >>> Irem >>> -- >>> 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.
Re: [gmx-users] -pbc nojump failure
Hi, Thanks for your suggestion. Unsurprisingly, the structure in nvt_water_frozen.tpr is also fragmented. Is there a way to use the input .pdb file as reference, somehow? Best, Irem > On Mar 31, 2016, at 12:45 AM, Tsjerk Wassenaar wrote: > > Hi Irem, > > Check the structure in nvt_water_frozen.tpr: > > gmx editconf -f nvt_water_frozen.tpr -o ref.pdb > > Cheers, > > Tsjerk > On Mar 31, 2016 00:04, "Irem Altan" wrote: > >> Hi, >> >> I am simulating a protein in its unit cell. I use the original .pdb file >> as an input, so the initial molecule is not fragmented. At the end of the >> simulation, I generate a .pdb file containing the trajectory of the protein >> as follows: >> >> gmx trjconv -f nvt_water_frozen.trr -s nvt_water_frozen.tpr -dt 20 -pbc >> nojump -o prot.pdb >> >> Despite the fact that I use -pbc nojump, I still get all the coordinates >> wrapped into the unit cell, and therefore the protein fragmented. What >> could be wrong? (I use GROMACS 5.1.2) >> >> Best, >> Irem >> -- >> 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.
Re: [gmx-users] -pbc nojump failure
You could try to fit first (-fit rot+trans) and fix pbc (-pbc nojump) later. Cheers, Fra On 31 March 2016 at 05:45, Tsjerk Wassenaar wrote: > Hi Irem, > > Check the structure in nvt_water_frozen.tpr: > > gmx editconf -f nvt_water_frozen.tpr -o ref.pdb > > Cheers, > > Tsjerk > On Mar 31, 2016 00:04, "Irem Altan" wrote: > > > Hi, > > > > I am simulating a protein in its unit cell. I use the original .pdb file > > as an input, so the initial molecule is not fragmented. At the end of the > > simulation, I generate a .pdb file containing the trajectory of the > protein > > as follows: > > > > gmx trjconv -f nvt_water_frozen.trr -s nvt_water_frozen.tpr -dt 20 -pbc > > nojump -o prot.pdb > > > > Despite the fact that I use -pbc nojump, I still get all the coordinates > > wrapped into the unit cell, and therefore the protein fragmented. What > > could be wrong? (I use GROMACS 5.1.2) > > > > Best, > > Irem > > -- > > 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.
Re: [gmx-users] -pbc nojump failure
Hi Irem, Check the structure in nvt_water_frozen.tpr: gmx editconf -f nvt_water_frozen.tpr -o ref.pdb Cheers, Tsjerk On Mar 31, 2016 00:04, "Irem Altan" wrote: > Hi, > > I am simulating a protein in its unit cell. I use the original .pdb file > as an input, so the initial molecule is not fragmented. At the end of the > simulation, I generate a .pdb file containing the trajectory of the protein > as follows: > > gmx trjconv -f nvt_water_frozen.trr -s nvt_water_frozen.tpr -dt 20 -pbc > nojump -o prot.pdb > > Despite the fact that I use -pbc nojump, I still get all the coordinates > wrapped into the unit cell, and therefore the protein fragmented. What > could be wrong? (I use GROMACS 5.1.2) > > Best, > Irem > -- > 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.
[gmx-users] -pbc nojump failure
Hi, I am simulating a protein in its unit cell. I use the original .pdb file as an input, so the initial molecule is not fragmented. At the end of the simulation, I generate a .pdb file containing the trajectory of the protein as follows: gmx trjconv -f nvt_water_frozen.trr -s nvt_water_frozen.tpr -dt 20 -pbc nojump -o prot.pdb Despite the fact that I use -pbc nojump, I still get all the coordinates wrapped into the unit cell, and therefore the protein fragmented. What could be wrong? (I use GROMACS 5.1.2) Best, Irem -- 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.
