Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using
Dear Dr. Warrem, Dear Tsjerk, Thank you for your emails. Following the suggestion of Dr. Warren I created several dir in which I applied different protocols on my system -- DIR1 -- 1) trjconv_mpi -s npt.tpr -f test.xtc -o test-nojump.xtc -pbc nojump (output System) 2) trjconv_mpi -s npt.tpr -f test-nojump.xtc -o test-center.xtc - center -n iindex.ndx (centering all the frames on Protein) (output system) 3) trjconv_mpi -s npt.tpr -f test-center.xtc -o test-compact.xtc -pbc mol -ur rect (output System) The related Figures are in the following link: http://wikisend.com/download/832038/Figtest1.zip #Comment: I obtain the same result also if a change rect with compact in the third step. -- DIR2 -- 1) trjconv_mpi -s npt.tpr -f test.xtc -o test-nojump.xtc -pbc nojump (output System) 2) trjconv_mpi -s npt.tpr -f test-nojump.xtc -o test-center.xtc - center -n iindex.ndx (centering all the frames on Protein) (output system) 3) trjconv_mpi -s npt.tpr -f test-center.xtc -o test-compact.xtc -pbc mol -ur rect (output System) 4) trjconv_mpi -s npt.tpr -f test-compact.xtc -o test-fit.xtc -fit progressive (fitting on Protein) The pics are here: http://wikisend.com/download/615140/FigTest2.zip #Comment: Here again, I obtain the same results as in the DIR1 but My protein has not translational motions. #Comment: In the step 2 i also centered the system on the Protein_DNA, nothing changes. Then, I tried different pbc/centering combination again but I strongly believe that fixing DNA-Protein complex is enough to obtain a good system. What would do you do to bring back the dsDNA inside the protein? In which step would you operate your command? Thanks in advance for your time. 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 Dallas Warren [dallas.war...@monash.edu] Sent: Thursday, May 22, 2014 1:40 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using Would suggest that each time you try a different workflow, do so in a new subdirectory and copy the required files into there. That way you ensure are using the files you think that you are. Will help those assisting to then post an image of the coordinate files at each step of the work flow, to see how things are changing, or not. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -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: Wednesday, 21 May 2014 11:07 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using Dear Tsjerk, No, it doesn't. (http://wikisend.com/download/324888/Post-nojump.png) I think that the first step need to be changed that's why I tried (whit no success) the flag -pbc whole. I'm still looking for a solution. Thanks again. 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 1:48 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using Hey Vito, After the first step, does the trajectory (say the last frame) look fine? If it does (everything nicely assembled), then after the second step, does it still look fine, and is it placed properly in the center of the box? Cheers, Tsjerk On Wed, May 21, 2014 at 12:50 PM, Vito Genna vito.ge...@iit.it wrote: 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
Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using
Hi Vito, Does npt.tpr correspond to the first frame of the trajectory and is the structure in npt.tpr correctly assembled? (editconf -f npt.tpr -o npt.tpr.pdb, and check). The only way that -pbc nojump can give a final frame in which the complex is separated is if the reference structure has them already separated. In that case, nothing you'll try will give you what you want. What I do in such cases is dump the first frame, using -pbc whole, and then shift the chains in Pymol according to the box vectors to have them together. Then I use the resulting structure as reference for processing the trajectory. Cheers, Tsjerk On Thu, May 22, 2014 at 10:59 AM, Vito Genna vito.ge...@iit.it wrote: Dear Dr. Warrem, Dear Tsjerk, Thank you for your emails. Following the suggestion of Dr. Warren I created several dir in which I applied different protocols on my system -- DIR1 -- 1) trjconv_mpi -s npt.tpr -f test.xtc -o test-nojump.xtc -pbc nojump (output System) 2) trjconv_mpi -s npt.tpr -f test-nojump.xtc -o test-center.xtc - center -n iindex.ndx (centering all the frames on Protein) (output system) 3) trjconv_mpi -s npt.tpr -f test-center.xtc -o test-compact.xtc -pbc mol -ur rect (output System) The related Figures are in the following link: http://wikisend.com/download/832038/Figtest1.zip #Comment: I obtain the same result also if a change rect with compact in the third step. -- DIR2 -- 1) trjconv_mpi -s npt.tpr -f test.xtc -o test-nojump.xtc -pbc nojump (output System) 2) trjconv_mpi -s npt.tpr -f test-nojump.xtc -o test-center.xtc - center -n iindex.ndx (centering all the frames on Protein) (output system) 3) trjconv_mpi -s npt.tpr -f test-center.xtc -o test-compact.xtc -pbc mol -ur rect (output System) 4) trjconv_mpi -s npt.tpr -f test-compact.xtc -o test-fit.xtc -fit progressive (fitting on Protein) The pics are here: http://wikisend.com/download/615140/FigTest2.zip #Comment: Here again, I obtain the same results as in the DIR1 but My protein has not translational motions. #Comment: In the step 2 i also centered the system on the Protein_DNA, nothing changes. Then, I tried different pbc/centering combination again but I strongly believe that fixing DNA-Protein complex is enough to obtain a good system. What would do you do to bring back the dsDNA inside the protein? In which step would you operate your command? Thanks in advance for your time. 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 Dallas Warren [dallas.war...@monash.edu] Sent: Thursday, May 22, 2014 1:40 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using Would suggest that each time you try a different workflow, do so in a new subdirectory and copy the required files into there. That way you ensure are using the files you think that you are. Will help those assisting to then post an image of the coordinate files at each step of the work flow, to see how things are changing, or not. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -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: Wednesday, 21 May 2014 11:07 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using Dear Tsjerk, No, it doesn't. (http://wikisend.com/download/324888/Post-nojump.png) I think that the first step need to be changed that's why I tried (whit no success) the flag -pbc whole. I'm still looking for a solution. Thanks again. 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
Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using
Dear Tsjerk, I exactly executed: editconf -f npt.tpr -o npt.pdb and I obtained a nicely assembled system (npt.pdb). Well, my system start to cross the boundaries after 20 ns of production phase so the npt.tpr is not the first frame of the trajectories that I trying to fix. After your email I've generated the md_0_1.tpr respecting your request with the command editconf -f md_0_1.tpr -o md_0_1.pdb and again I obtain a well assembled system. The trajectories that I want to fix, is obtained from: trjconv_mpi -f md_0_1.part0001.xtc -o test.xtc -s md_0_1.tpr -skip 100 To be consistent in the procedure, I did again all the steps (-pbc nojump, -center, -compact -ur rect) using the md_0_1.tpr. The result is exactly the same! I'm really losing hope! I will try the Pymol strategy also. Thank you for your hints. 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: Thursday, May 22, 2014 11:10 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using Hi Vito, Does npt.tpr correspond to the first frame of the trajectory and is the structure in npt.tpr correctly assembled? (editconf -f npt.tpr -o npt.tpr.pdb, and check). The only way that -pbc nojump can give a final frame in which the complex is separated is if the reference structure has them already separated. In that case, nothing you'll try will give you what you want. What I do in such cases is dump the first frame, using -pbc whole, and then shift the chains in Pymol according to the box vectors to have them together. Then I use the resulting structure as reference for processing the trajectory. Cheers, Tsjerk On Thu, May 22, 2014 at 10:59 AM, Vito Genna vito.ge...@iit.it wrote: Dear Dr. Warrem, Dear Tsjerk, Thank you for your emails. Following the suggestion of Dr. Warren I created several dir in which I applied different protocols on my system -- DIR1 -- 1) trjconv_mpi -s npt.tpr -f test.xtc -o test-nojump.xtc -pbc nojump (output System) 2) trjconv_mpi -s npt.tpr -f test-nojump.xtc -o test-center.xtc - center -n iindex.ndx (centering all the frames on Protein) (output system) 3) trjconv_mpi -s npt.tpr -f test-center.xtc -o test-compact.xtc -pbc mol -ur rect (output System) The related Figures are in the following link: http://wikisend.com/download/832038/Figtest1.zip #Comment: I obtain the same result also if a change rect with compact in the third step. -- DIR2 -- 1) trjconv_mpi -s npt.tpr -f test.xtc -o test-nojump.xtc -pbc nojump (output System) 2) trjconv_mpi -s npt.tpr -f test-nojump.xtc -o test-center.xtc - center -n iindex.ndx (centering all the frames on Protein) (output system) 3) trjconv_mpi -s npt.tpr -f test-center.xtc -o test-compact.xtc -pbc mol -ur rect (output System) 4) trjconv_mpi -s npt.tpr -f test-compact.xtc -o test-fit.xtc -fit progressive (fitting on Protein) The pics are here: http://wikisend.com/download/615140/FigTest2.zip #Comment: Here again, I obtain the same results as in the DIR1 but My protein has not translational motions. #Comment: In the step 2 i also centered the system on the Protein_DNA, nothing changes. Then, I tried different pbc/centering combination again but I strongly believe that fixing DNA-Protein complex is enough to obtain a good system. What would do you do to bring back the dsDNA inside the protein? In which step would you operate your command? Thanks in advance for your time. 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 Dallas Warren [dallas.war...@monash.edu] Sent: Thursday, May 22, 2014 1:40 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using Would suggest that each time you try a different workflow, do so in a new subdirectory and copy the required files into there. That way you ensure are using the files you think that you are. Will help those assisting to then post an image of the coordinate
Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using
Hey Vito, Don't use -skip. And add -pbc nojump to that first run of trjconv: trjconv_mpi -f md_0_1.part0001.xtc -o test.xtc -s md_0_1.tpr -pbc nojump Then have a look at the last frame to see if it's good. If md_0_1.tpr is assembled properly, then the last frame should be too, provided the assembly did not fall apart (in which case you're in real trouble). Cheers, Tsjerk On Thu, May 22, 2014 at 3:01 PM, Vito Genna vito.ge...@iit.it wrote: Dear Tsjerk, I exactly executed: editconf -f npt.tpr -o npt.pdb and I obtained a nicely assembled system (npt.pdb). Well, my system start to cross the boundaries after 20 ns of production phase so the npt.tpr is not the first frame of the trajectories that I trying to fix. After your email I've generated the md_0_1.tpr respecting your request with the command editconf -f md_0_1.tpr -o md_0_1.pdb and again I obtain a well assembled system. The trajectories that I want to fix, is obtained from: trjconv_mpi -f md_0_1.part0001.xtc -o test.xtc -s md_0_1.tpr -skip 100 To be consistent in the procedure, I did again all the steps (-pbc nojump, -center, -compact -ur rect) using the md_0_1.tpr. The result is exactly the same! I'm really losing hope! I will try the Pymol strategy also. Thank you for your hints. 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: Thursday, May 22, 2014 11:10 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using Hi Vito, Does npt.tpr correspond to the first frame of the trajectory and is the structure in npt.tpr correctly assembled? (editconf -f npt.tpr -o npt.tpr.pdb, and check). The only way that -pbc nojump can give a final frame in which the complex is separated is if the reference structure has them already separated. In that case, nothing you'll try will give you what you want. What I do in such cases is dump the first frame, using -pbc whole, and then shift the chains in Pymol according to the box vectors to have them together. Then I use the resulting structure as reference for processing the trajectory. Cheers, Tsjerk On Thu, May 22, 2014 at 10:59 AM, Vito Genna vito.ge...@iit.it wrote: Dear Dr. Warrem, Dear Tsjerk, Thank you for your emails. Following the suggestion of Dr. Warren I created several dir in which I applied different protocols on my system -- DIR1 -- 1) trjconv_mpi -s npt.tpr -f test.xtc -o test-nojump.xtc -pbc nojump (output System) 2) trjconv_mpi -s npt.tpr -f test-nojump.xtc -o test-center.xtc - center -n iindex.ndx (centering all the frames on Protein) (output system) 3) trjconv_mpi -s npt.tpr -f test-center.xtc -o test-compact.xtc -pbc mol -ur rect (output System) The related Figures are in the following link: http://wikisend.com/download/832038/Figtest1.zip #Comment: I obtain the same result also if a change rect with compact in the third step. -- DIR2 -- 1) trjconv_mpi -s npt.tpr -f test.xtc -o test-nojump.xtc -pbc nojump (output System) 2) trjconv_mpi -s npt.tpr -f test-nojump.xtc -o test-center.xtc - center -n iindex.ndx (centering all the frames on Protein) (output system) 3) trjconv_mpi -s npt.tpr -f test-center.xtc -o test-compact.xtc -pbc mol -ur rect (output System) 4) trjconv_mpi -s npt.tpr -f test-compact.xtc -o test-fit.xtc -fit progressive (fitting on Protein) The pics are here: http://wikisend.com/download/615140/FigTest2.zip #Comment: Here again, I obtain the same results as in the DIR1 but My protein has not translational motions. #Comment: In the step 2 i also centered the system on the Protein_DNA, nothing changes. Then, I tried different pbc/centering combination again but I strongly believe that fixing DNA-Protein complex is enough to obtain a good system. What would do you do to bring back the dsDNA inside the protein? In which step would you operate your command? Thanks in advance for your time. 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
Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using
Dear Tsjerk, I'm glad to write to you because it works fine! The system is now perfectly assemble. -pbc nojump using the md_0_1.tpr is enough to rebuild the system. The only problem is the water that diffuses leaving the protein. I think that with the -center flag i can bring back H20 inside the box. Thank you so much! I was doing a lot of attempts! Cheers 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 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: Thursday, May 22, 2014 4:06 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using Hey Vito, Don't use -skip. And add -pbc nojump to that first run of trjconv: trjconv_mpi -f md_0_1.part0001.xtc -o test.xtc -s md_0_1.tpr -pbc nojump Then have a look at the last frame to see if it's good. If md_0_1.tpr is assembled properly, then the last frame should be too, provided the assembly did not fall apart (in which case you're in real trouble). Cheers, Tsjerk On Thu, May 22, 2014 at 3:01 PM, Vito Genna vito.ge...@iit.it wrote: Dear Tsjerk, I exactly executed: editconf -f npt.tpr -o npt.pdb and I obtained a nicely assembled system (npt.pdb). Well, my system start to cross the boundaries after 20 ns of production phase so the npt.tpr is not the first frame of the trajectories that I trying to fix. After your email I've generated the md_0_1.tpr respecting your request with the command editconf -f md_0_1.tpr -o md_0_1.pdb and again I obtain a well assembled system. The trajectories that I want to fix, is obtained from: trjconv_mpi -f md_0_1.part0001.xtc -o test.xtc -s md_0_1.tpr -skip 100 To be consistent in the procedure, I did again all the steps (-pbc nojump, -center, -compact -ur rect) using the md_0_1.tpr. The result is exactly the same! I'm really losing hope! I will try the Pymol strategy also. Thank you for your hints. 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: Thursday, May 22, 2014 11:10 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using Hi Vito, Does npt.tpr correspond to the first frame of the trajectory and is the structure in npt.tpr correctly assembled? (editconf -f npt.tpr -o npt.tpr.pdb, and check). The only way that -pbc nojump can give a final frame in which the complex is separated is if the reference structure has them already separated. In that case, nothing you'll try will give you what you want. What I do in such cases is dump the first frame, using -pbc whole, and then shift the chains in Pymol according to the box vectors to have them together. Then I use the resulting structure as reference for processing the trajectory. Cheers, Tsjerk On Thu, May 22, 2014 at 10:59 AM, Vito Genna vito.ge...@iit.it wrote: Dear Dr. Warrem, Dear Tsjerk, Thank you for your emails. Following the suggestion of Dr. Warren I created several dir in which I applied different protocols on my system -- DIR1 -- 1) trjconv_mpi -s npt.tpr -f test.xtc -o test-nojump.xtc -pbc nojump (output System) 2) trjconv_mpi -s npt.tpr -f test-nojump.xtc -o test-center.xtc - center -n iindex.ndx (centering all the frames on Protein) (output system) 3) trjconv_mpi -s npt.tpr -f test-center.xtc -o test-compact.xtc -pbc mol -ur rect (output System) The related Figures are in the following link: http://wikisend.com/download/832038/Figtest1.zip #Comment: I obtain the same result also if a change rect with compact in the third step. -- DIR2 -- 1) trjconv_mpi -s npt.tpr -f test.xtc -o test-nojump.xtc -pbc nojump (output System) 2) trjconv_mpi -s npt.tpr -f test-nojump.xtc -o test-center.xtc - center -n iindex.ndx (centering all the frames on Protein) (output system) 3) trjconv_mpi -s npt.tpr -f test-center.xtc -o test-compact.xtc -pbc mol -ur rect (output System) 4) trjconv_mpi -s npt.tpr -f test-compact.xtc -o test
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 DNAProtein/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
Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using
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
Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using
Dear Tsjerk, No, it doesn't. (http://wikisend.com/download/324888/Post-nojump.png) I think that the first step need to be changed that's why I tried (whit no success) the flag -pbc whole. I'm still looking for a solution. Thanks again. 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 1:48 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using Hey Vito, After the first step, does the trajectory (say the last frame) look fine? If it does (everything nicely assembled), then after the second step, does it still look fine, and is it placed properly in the center of the box? Cheers, Tsjerk On Wed, May 21, 2014 at 12:50 PM, Vito Genna vito.ge...@iit.it wrote: 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 -- 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] How to efficiently fix pbc trajectories problems for VMD using
On Wed, May 21, 2014 at 6:37 PM, Vito Genna vito.ge...@iit.it wrote: Dear Tsjerk, No, it doesn't. (http://wikisend.com/download/324888/Post-nojump.png) I think that the first step need to be changed that's why I tried (whit no success) the flag -pbc whole. I'm still looking for a solution. It seems that the tpr you are supplying has PBC in it. I assume the first tpr should be generated from PBC free structure. That is the understanding I had. Correct me if I am wrong. Chandan Thanks again. 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 1:48 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using Hey Vito, After the first step, does the trajectory (say the last frame) look fine? If it does (everything nicely assembled), then after the second step, does it still look fine, and is it placed properly in the center of the box? Cheers, Tsjerk On Wed, May 21, 2014 at 12:50 PM, Vito Genna vito.ge...@iit.it wrote: 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 -- 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. -- -- Chandan Kumar Choudhury National Chemical Laboratory, Pune India -- 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] How to efficiently fix pbc trajectories problems for VMD using
That doesn't make sense..., sorry. Cheers, Tsjerk On May 21, 2014 6:40 PM, Chandan Choudhury iitd...@gmail.com wrote: On Wed, May 21, 2014 at 6:37 PM, Vito Genna vito.ge...@iit.it wrote: Dear Tsjerk, No, it doesn't. (http://wikisend.com/download/324888/Post-nojump.png) I think that the first step need to be changed that's why I tried (whit no success) the flag -pbc whole. I'm still looking for a solution. It seems that the tpr you are supplying has PBC in it. I assume the first tpr should be generated from PBC free structure. That is the understanding I had. Correct me if I am wrong. Chandan Thanks again. 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 1:48 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using Hey Vito, After the first step, does the trajectory (say the last frame) look fine? If it does (everything nicely assembled), then after the second step, does it still look fine, and is it placed properly in the center of the box? Cheers, Tsjerk On Wed, May 21, 2014 at 12:50 PM, Vito Genna vito.ge...@iit.it wrote: 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 -- 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. -- -- Chandan Kumar Choudhury National Chemical Laboratory, Pune India -- 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] How to efficiently fix pbc trajectories problems for VMD using
Would suggest that each time you try a different workflow, do so in a new subdirectory and copy the required files into there. That way you ensure are using the files you think that you are. Will help those assisting to then post an image of the coordinate files at each step of the work flow, to see how things are changing, or not. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -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: Wednesday, 21 May 2014 11:07 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using Dear Tsjerk, No, it doesn't. (http://wikisend.com/download/324888/Post-nojump.png) I think that the first step need to be changed that's why I tried (whit no success) the flag -pbc whole. I'm still looking for a solution. Thanks again. 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 1:48 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using Hey Vito, After the first step, does the trajectory (say the last frame) look fine? If it does (everything nicely assembled), then after the second step, does it still look fine, and is it placed properly in the center of the box? Cheers, Tsjerk On Wed, May 21, 2014 at 12:50 PM, Vito Genna vito.ge...@iit.it wrote: 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 -- 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] How to efficiently fix pbc trajectories problems for VMD using
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 DNAProtein/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
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 DNAProtein/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
Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using
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 DNAProtein/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
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 DNAProtein/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
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.
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.
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
Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using
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
Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using
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
Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using
HI Andrea, Thank you for your suggestion. I'll let you know. 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 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Andrea Spitaleri [andrea.spital...@iit.it] Sent: Monday, May 19, 2014 5:43 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using 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
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
