Re: [gmx-users] pbc problem
On Tue, Oct 29, 2013 at 5:02 PM, shahab shariati shahab.shari...@gmail.comwrote: Dear Mark Very thanks for your reply To make this clear, center the trajectory on the water and watch the time evolution in some visualization program. I did your suggestion (center the trajectory on the water). Again, drug molecule is in region (1)in some frames and is in region (4) in other frames. With pbc = xyz, you do not have two chunks of water. You have one chunk of water. Where you put the box for visualization is irrelevant to the simulation. You could align one of the box sides with one of the membrane surfaces, and now you will see only one chunk of membrane, and one chunk of water. In that chunk of water the drug goes wherever diffusion takes it, just like it did inside the membrane. Mark -- Dear Justin Very thanks for your attention As has already been stated several times, there is no problem at all. The outcome is completely normal, and there are not discrete regions (1) and (4). It is a continuous block of water via PBC. The molecule can freely diffuse throughout it. If outcome is completely normal, Can I use this structure for pmf calculation. I want to calculate potential of mean force, delta G, as a function of the distance between the centers of mass of drug and the centers of mass of bilayer. Best wishes for you. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] pbc problem
On 10/29/13 12:02 PM, shahab shariati wrote: Dear Mark Very thanks for your reply To make this clear, center the trajectory on the water and watch the time evolution in some visualization program. I did your suggestion (center the trajectory on the water). Again, drug molecule is in region (1)in some frames and is in region (4) in other frames. -- Dear Justin Very thanks for your attention As has already been stated several times, there is no problem at all. The outcome is completely normal, and there are not discrete regions (1) and (4). It is a continuous block of water via PBC. The molecule can freely diffuse throughout it. If outcome is completely normal, Can I use this structure for pmf calculation. I want to calculate potential of mean force, delta G, as a function of the distance between the centers of mass of drug and the centers of mass of bilayer. Given the inherent symmetry of the system, yes. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] pbc problem
On 10/27/13 8:16 AM, shahab shariati wrote: Dear Justin I want to study translocation of drug molecule in lipid bilayer. My gro file after minimization is em2.gro. After NPT-MD simulation, I obtained npt.gro and 0.xtc files. When I see trajectory by vmd, there are some things abnormal. I guess there is pbc problem. I attached these 3 files. Please after viewing them, tell me is my guess true. If yes, please guide me how to fix it. If no, please tell me what is problem? https://www.dropbox.com/s/d0hppxdngj7xwst/em2.gro https://www.dropbox.com/s/gnqf6fuxwwj0zzt/npt.gro https://www.dropbox.com/s/w899y86mhp0ysbo/0.xtc Images are better, especially ones that don't have to be downloaded. I'm not going to download a potentially large .xtc file, sorry. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] pbc problem
Hi Shahab, What about running trjconv -pbc mol with a .tpr as input file? Cheers, Tsjerk On Sun, Oct 27, 2013 at 3:24 PM, shahab shariati shahab.shari...@gmail.comwrote: Dear Justin I attached images related to before (em2.gro) and after equilibration. https://www.dropbox.com/s/yjkyj5ycshvp20u/images.docx -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] pbc problem
On 10/27/13 12:05 PM, shahab shariati wrote: Dear Tsjerk Wassenaar Very very thanks for your reply. I used trjconv -pbc mol. pbc problem was solved only for lipid molecules. When I see new trajectory by vmd, there are some problesm about drug molecule. https://www.dropbox.com/s/xq4s6az17buhvb8/images-2.docx If I show my system as 4 regions, my system before equilibration is as fallows: region (1): water + drug region (2): top leaflet of bilayer region (3): bottom leaflet of bilayer region (4): water After equilibration, drug molecule exits region (1) and enters region (4), alternately. On the other hand, drug molecule is in region (1)in some frames and is in region (4) in other frames. Please tell me how to fix it? Is this issue (about drug molecule) pbc problem? As has already been stated several times, there is no problem at all. The outcome is completely normal, and there are not discrete regions (1) and (4). It is a continuous block of water via PBC. The molecule can freely diffuse throughout it. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] pbc problem
On Oct 24, 2013 8:10 AM, shahab shariati shahab.shari...@gmail.com wrote: Dear jkrieger I used 2 times trjconv tool: 1) trjconv -f npt.xtc -s npt.tpr -n index.ndx -o 2npt.xtc -pbc nojump 2) trjconv -f 2npt.xtc -s npt.tpr -n index.ndx -o 3npt.xtc -pbc mol -center Dear Mark I selected all lipid atoms for centering. With my manner, pbc problem was solved just for lipids and not for drug molecule which is put inside water molecules in top leaflet. This pbc problem cause to drug molecule be in top and bottom leaflets, while I want to study translocation of the drug molecule from water to lipid bilayer. I want to solve this problem for drug molecule. There is only one water region, so upper and lower don't mean much. If you just want to see the drug and bilayer in the same PBC cell, then center on something that is central. Mark If my manner is wrong, please tell me true way. Best wishes. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] pbc problem
On 10/24/13 10:57 AM, shahab shariati wrote: Dear Mark Thank for your reply. If I show my system as 4 regions, my system before equilibration is as fallows: region (1): water + drug region (2): top leaflet of bilayer region (3): bottom leaflet of bilayer region (4): water After equilibration, drug molecule exits region (1) and enters region (4). Please tell me how to fix it? Which options of trjconv are appropriate for this problem? So the drug diffused within a continuous block of solvent, is that a problem? It shouldn't be, since the system is periodic. In some cases, trjconv magic doesn't work because it shouldn't. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] pbc problem
As Justin said, there is no actual division between region 1 and 4. Apparently you got the free diffusion you asked for! :-) Mark On Thu, Oct 24, 2013 at 4:57 PM, shahab shariati shahab.shari...@gmail.comwrote: Dear Mark Thank for your reply. If I show my system as 4 regions, my system before equilibration is as fallows: region (1): water + drug region (2): top leaflet of bilayer region (3): bottom leaflet of bilayer region (4): water After equilibration, drug molecule exits region (1) and enters region (4). Please tell me how to fix it? Which options of trjconv are appropriate for this problem? Best wishes -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] pbc problem
I usually use -pbc nojump for my protein simulations and this works every time. Dear gromacs users My system contains DOPC + CHOLESTEROLO + WATER + drug molecules in a rectangular box. I put drug molecule in 2 position: a) drug in the center of bilayer membrane, b) drug inside water molecules in top leaflet. For both positions, I did energy minimization successfully with following mdp file. -- ; Parameters describing what to do, when to stop and what to save integrator= steep; Algorithm (steep = steepest descent minimization) emtol= 1000.0 ; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps= 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom nstlist= 1; Frequency to update the neighbor list and long range forces ns_type= grid; Method to determine neighbor list (simple, grid) rlist= 1.2; Cut-off for making neighbor list (short range forces) coulombtype= PME; Treatment of long range electrostatic interactions rcoulomb= 1.2; Short-range electrostatic cut-off rvdw= 1.2; Short-range Van der Waals cut-off pbc= xyz ; Periodic Boundary Conditions --- After energy minimization, I saw obtained file (em.gro) by VMD. All things were true and intact. For both positions, I did equilibration in NPT ensemble with following mdp file. --- ; Run parameters integrator= md; leap-frog integrator nsteps= 25; 2 * 50 = 1000 ps (1 ns) dt= 0.002; 2 fs ; Output control nstxout= 100; save coordinates every 0.2 ps nstvout= 100; save velocities every 0.2 ps nstxtcout = 100; xtc compressed trajectory output every 2 ps nstenergy= 100; save energies every 0.2 ps nstlog= 100; update log file every 0.2 ps energygrps = CHOL DOPC drg SOL ; Bond parameters continuation= no; Restarting after NVT constraint_algorithm = lincs; holonomic constraints constraints= all-bonds; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1; accuracy of LINCS lincs_order= 4; also related to accuracy ; Neighborsearching ns_type= grid; search neighboring grid cels nstlist= 5; 10 fs rlist= 1.0; short-range neighborlist cutoff (in nm) rcoulomb= 1.0; short-range electrostatic cutoff (in nm) rvdw= 1.0; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype= PME; Particle Mesh Ewald for long-range electrostatics pme_order= 4; cubic interpolation fourierspacing= 0.16; grid spacing for FFT ; Temperature coupling is on tcoupl= V-rescale; More accurate thermostat tc-grps= CHOL_DOPCdrg SOL; three coupling groups - more accurate tau_t= 0.50.5 0.5 ; time constant, in ps ref_t= 323 323 323 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl= Parrinello-Rahman; Pressure coupling on in NPT pcoupltype= semiisotropic; uniform scaling of x-y box vectors, independent z tau_p= 5.0; time constant, in ps ref_p= 1.01.0; reference pressure, x-y, z (in bar) compressibility = 4.5e-54.5e-5; isothermal compressibility, bar^-1 ; Periodic boundary conditions pbc= xyz; 3-D PBC ; Dispersion correction DispCorr= EnerPres; account for cut-off vdW scheme ; Velocity generation gen_vel= yes; assign velocities from Maxwell distribution gen_temp= 323; temperature for Maxwell distribution gen_seed= -1; generate a random seed ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 1 comm-mode = Linear comm-grps = CHOL_DOPC_drg SOL ; Scale COM of reference coordinates refcoord_scaling = com --- For 2 positions, I chechked tempreture and pressure fluctuation and box dimention during equilibration. All things were good. When I saw trajectory by VMD (npt.gro and npt xtc), I had pbc problem (some atoms leave box and enter the box in opposit direction). For position (a): I corrected pbc problem by
Re: [gmx-users] pbc problem
Center on a particular lipid? Or head group? Mark On Oct 23, 2013 6:13 PM, shahab shariati shahab.shari...@gmail.com wrote: Dear gromacs users My system contains DOPC + CHOLESTEROLO + WATER + drug molecules in a rectangular box. I put drug molecule in 2 position: a) drug in the center of bilayer membrane, b) drug inside water molecules in top leaflet. For both positions, I did energy minimization successfully with following mdp file. -- ; Parameters describing what to do, when to stop and what to save integrator= steep; Algorithm (steep = steepest descent minimization) emtol= 1000.0 ; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps= 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom nstlist= 1; Frequency to update the neighbor list and long range forces ns_type= grid; Method to determine neighbor list (simple, grid) rlist= 1.2; Cut-off for making neighbor list (short range forces) coulombtype= PME; Treatment of long range electrostatic interactions rcoulomb= 1.2; Short-range electrostatic cut-off rvdw= 1.2; Short-range Van der Waals cut-off pbc= xyz ; Periodic Boundary Conditions --- After energy minimization, I saw obtained file (em.gro) by VMD. All things were true and intact. For both positions, I did equilibration in NPT ensemble with following mdp file. --- ; Run parameters integrator= md; leap-frog integrator nsteps= 25; 2 * 50 = 1000 ps (1 ns) dt= 0.002; 2 fs ; Output control nstxout= 100; save coordinates every 0.2 ps nstvout= 100; save velocities every 0.2 ps nstxtcout = 100; xtc compressed trajectory output every 2 ps nstenergy= 100; save energies every 0.2 ps nstlog= 100; update log file every 0.2 ps energygrps = CHOL DOPC drg SOL ; Bond parameters continuation= no; Restarting after NVT constraint_algorithm = lincs; holonomic constraints constraints= all-bonds; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1; accuracy of LINCS lincs_order= 4; also related to accuracy ; Neighborsearching ns_type= grid; search neighboring grid cels nstlist= 5; 10 fs rlist= 1.0; short-range neighborlist cutoff (in nm) rcoulomb= 1.0; short-range electrostatic cutoff (in nm) rvdw= 1.0; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype= PME; Particle Mesh Ewald for long-range electrostatics pme_order= 4; cubic interpolation fourierspacing= 0.16; grid spacing for FFT ; Temperature coupling is on tcoupl= V-rescale; More accurate thermostat tc-grps= CHOL_DOPCdrg SOL; three coupling groups - more accurate tau_t= 0.50.5 0.5 ; time constant, in ps ref_t= 323 323 323 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl= Parrinello-Rahman; Pressure coupling on in NPT pcoupltype= semiisotropic; uniform scaling of x-y box vectors, independent z tau_p= 5.0; time constant, in ps ref_p= 1.01.0; reference pressure, x-y, z (in bar) compressibility = 4.5e-54.5e-5; isothermal compressibility, bar^-1 ; Periodic boundary conditions pbc= xyz; 3-D PBC ; Dispersion correction DispCorr= EnerPres; account for cut-off vdW scheme ; Velocity generation gen_vel= yes; assign velocities from Maxwell distribution gen_temp= 323; temperature for Maxwell distribution gen_seed= -1; generate a random seed ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 1 comm-mode = Linear comm-grps = CHOL_DOPC_drg SOL ; Scale COM of reference coordinates refcoord_scaling = com --- For 2 positions, I chechked tempreture and pressure fluctuation and box dimention during equilibration. All things were good. When I saw trajectory by VMD (npt.gro and npt xtc), I had pbc problem (some atoms leave box and enter the box in opposit direction). For
Re: [gmx-users] PBC problem
Hi Yutian Yang, Yes. That is, if the chain is interacting with itself. If it remains curled up, then it won't be a problem. Cheers, Tsjerk On Thu, Jun 27, 2013 at 10:10 PM, Yutian Yang yyan...@syr.edu wrote: Hi all, I have a question about PBC. If I have a polymer chain that is longer than the box length, will the properties of the chain change because the tail of the chain may interact with the head of the chain due to PBC? Thank you! Yutian -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] pbc problem
On 4/14/13 11:21 PM, Kieu Thu Nguyen wrote: Thank Justin ! I used the command editconf -center and i saw my membrane was in center of the box. I am stupid in that how putting the bilayer in a periodic image (instead between two periodic images as it was). Can you give me some instructions ? Many thanks ! I don't know what it is that you did before, so I can't say. In principle, one could have two leaflets at periodic boundaries along the z-axis and it's exactly the same as having an intact membrane in the center of the box from the standpoint of dynamics. For building membrane protein systems, however, that's less than convenient. -Justin On Fri, Apr 12, 2013 at 6:52 PM, Justin Lemkul jalem...@vt.edu wrote: On Fri, Apr 12, 2013 at 7:48 AM, Kieu Thu Nguyen kieuthu2...@gmail.com wrote: Dear All, I made a POPC bilayer and carried out embedding a protein into this membrane. But the fatal error has appeared : Fatal error: Something is wrong with your membrane. Max and min z values are 12.342000 and 0.016000. Maybe your membrane is not centered in the box, but located at the box edge in the z-direction, so that one membrane is distributed over two periodic box images. Another possibility is that your water layer is not thick enough. I think my bilayer stay at between two periodic images. What should i do to put it in corrected position ? It should be a very simple matter of visualization. Use editconf -center to place the membrane wherever you want within the unit cell. You can remove the uncertainty (I think is weak compared to I know) by looking at the box vectors and then numerically determining the center of the membrane with g_traj. That should provide you with all the information you need to determine what's going on. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] pbc problem
Thank Justin ! I used the command editconf -center and i saw my membrane was in center of the box. I am stupid in that how putting the bilayer in a periodic image (instead between two periodic images as it was). Can you give me some instructions ? Many thanks ! On Fri, Apr 12, 2013 at 6:52 PM, Justin Lemkul jalem...@vt.edu wrote: On Fri, Apr 12, 2013 at 7:48 AM, Kieu Thu Nguyen kieuthu2...@gmail.com wrote: Dear All, I made a POPC bilayer and carried out embedding a protein into this membrane. But the fatal error has appeared : Fatal error: Something is wrong with your membrane. Max and min z values are 12.342000 and 0.016000. Maybe your membrane is not centered in the box, but located at the box edge in the z-direction, so that one membrane is distributed over two periodic box images. Another possibility is that your water layer is not thick enough. I think my bilayer stay at between two periodic images. What should i do to put it in corrected position ? It should be a very simple matter of visualization. Use editconf -center to place the membrane wherever you want within the unit cell. You can remove the uncertainty (I think is weak compared to I know) by looking at the box vectors and then numerically determining the center of the membrane with g_traj. That should provide you with all the information you need to determine what's going on. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] pbc problem
On Fri, Apr 12, 2013 at 7:48 AM, Kieu Thu Nguyen kieuthu2...@gmail.comwrote: Dear All, I made a POPC bilayer and carried out embedding a protein into this membrane. But the fatal error has appeared : Fatal error: Something is wrong with your membrane. Max and min z values are 12.342000 and 0.016000. Maybe your membrane is not centered in the box, but located at the box edge in the z-direction, so that one membrane is distributed over two periodic box images. Another possibility is that your water layer is not thick enough. I think my bilayer stay at between two periodic images. What should i do to put it in corrected position ? It should be a very simple matter of visualization. Use editconf -center to place the membrane wherever you want within the unit cell. You can remove the uncertainty (I think is weak compared to I know) by looking at the box vectors and then numerically determining the center of the membrane with g_traj. That should provide you with all the information you need to determine what's going on. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] pbc problem
hi, all My protein has 16 subunits. After I use trjconv '-pbc nojump' to remove the jump in the whole protein, there are no jump to each subunits. However, when i check pdb file of the first frame, it is shown that the subunits are not in right position. The area of interface between some subunits is zero, but it should not be. Could you give me some suggestions how to solve this problem? Try some of the other options to trjconv. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] pbc problem
On 10/16/2007 2:31 AM, tangxuan wrote: Dear all, If pbc is full or xyz in mdp file, do i need to use the trjconv -pbc nojump to remove the jump when the protein is separate in the box after simulation and I want to calculate the rmsd of the protein? IT is not necessary to use trjconv -pbc before running most gromacs analysis tools. they have built-in support to move atom back if they appear at the other side. What is difference of use of pbc in mdp file and in trjconv -pbc nojump? they are two separate stuff: specify pbc=full or pbc=xyz in mdp indicate that the simulation is carried out with PBC so that atoms which moves out of the box will appear on the other side of the box; trjconv -pbc nojump is a post-processing step, meant for visualization or analysis tools not provided by GROMACS. Thank you!! Tang Jiaowei ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] PBC problem
Hi Yuguang,
Gromacs should automatically fix the box to meet the requirements
during an mdrun with pressure coupling (but does sometimes fail).
There is also a certain tolerance in gromacs for the deviations.
Anyway.., you can download a version of GMX3.2.1 from
http://nmr.chem.uu.nl/~tsjerk/GMX/gromacs-3.2.1-rtc.tgz
in which I modified editconf.c (and pbc.c/pbc.h) to have an option for
changing any triclinic box into a box which conforms to the gromacs
rules. Maybe you just want to get the parts of the code involved and
transfer them to GMX3.3.1, which should be quite straightforward. The
developers are welcome to incorporate the option/code if they like to
include it. The editconf option I added is -fix. Note that editconf
will still issue a warning about the skewness of the box, but on a
'fixed' structure, that should not occur anymore.
Hope it helps,
Tsjerk
On 5/16/07, Mu Yuguang (Dr) [EMAIL PROTECTED] wrote:
Thanks Tsjerk,
Probably because we use pressure coupling and the box size is deformed.
Best regards
Yuguang
Dr. Yuguang Mu
Assistant Professor
School of Biological Sciences
Nanyang Technological University
60 Nanyang Drive Singapore 637551 Tel: +65-63162885 Fax: +65-67913856
http://genome.sbs.ntu.edu.sg/Staff/YGMu/index.php
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Tsjerk Wassenaar
Sent: Wednesday, May 16, 2007 12:49 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] PBC problem
Hi Yuguang,
Warning: Triclinic box is too skewed.
Box (3x3):
Box[0]={ 6.46530e+00, 0.0e+00, 0.0e+00}
Box[1]={ 2.14552e+00, 6.10274e+00, 0.0e+00}
Box[2]={-2.14464e+00, 3.05200e+00, 5.24664e+00}
This is not a rhombic dodecahedron.
CRYST1 64.653 64.689 64.375 70.32 109.46 70.63 P 1 1
This shows that the second vector is larger than the first, thus
violating the gromacs rules for proper boxes (manual chapter 3;
although it could be handled a bit more liberally, especially in the
analysis tools).
Cheers,
Tsjerk
--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
___
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___
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Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
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RE: [gmx-users] PBC problem
Hi Tsjerk,
Thanks. I will try that.
Best regards
Yuguang
Dr. Yuguang Mu
Assistant Professor
School of Biological Sciences
Nanyang Technological University
60 Nanyang Drive Singapore 637551 Tel: +65-63162885 Fax: +65-67913856
http://genome.sbs.ntu.edu.sg/Staff/YGMu/index.php
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Tsjerk Wassenaar
Sent: Wednesday, May 16, 2007 4:41 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] PBC problem
Hi Yuguang,
Gromacs should automatically fix the box to meet the requirements
during an mdrun with pressure coupling (but does sometimes fail).
There is also a certain tolerance in gromacs for the deviations.
Anyway.., you can download a version of GMX3.2.1 from
http://nmr.chem.uu.nl/~tsjerk/GMX/gromacs-3.2.1-rtc.tgz
in which I modified editconf.c (and pbc.c/pbc.h) to have an option for
changing any triclinic box into a box which conforms to the gromacs
rules. Maybe you just want to get the parts of the code involved and
transfer them to GMX3.3.1, which should be quite straightforward. The
developers are welcome to incorporate the option/code if they like to
include it. The editconf option I added is -fix. Note that editconf
will still issue a warning about the skewness of the box, but on a
'fixed' structure, that should not occur anymore.
Hope it helps,
Tsjerk
On 5/16/07, Mu Yuguang (Dr) [EMAIL PROTECTED] wrote:
Thanks Tsjerk,
Probably because we use pressure coupling and the box size is
deformed.
Best regards
Yuguang
Dr. Yuguang Mu
Assistant Professor
School of Biological Sciences
Nanyang Technological University
60 Nanyang Drive Singapore 637551 Tel: +65-63162885 Fax: +65-67913856
http://genome.sbs.ntu.edu.sg/Staff/YGMu/index.php
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Tsjerk Wassenaar
Sent: Wednesday, May 16, 2007 12:49 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] PBC problem
Hi Yuguang,
Warning: Triclinic box is too skewed.
Box (3x3):
Box[0]={ 6.46530e+00, 0.0e+00, 0.0e+00}
Box[1]={ 2.14552e+00, 6.10274e+00, 0.0e+00}
Box[2]={-2.14464e+00, 3.05200e+00, 5.24664e+00}
This is not a rhombic dodecahedron.
CRYST1 64.653 64.689 64.375 70.32 109.46 70.63 P 1
1
This shows that the second vector is larger than the first, thus
violating the gromacs rules for proper boxes (manual chapter 3;
although it could be handled a bit more liberally, especially in the
analysis tools).
Cheers,
Tsjerk
--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before
posting!
Please don't post (un)subscribe requests to the list. Use the
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Can't post? Read http://www.gromacs.org/mailing_lists/users.php
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before
posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before
posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
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RE: [gmx-users] PBC problem
Thanks Tsjerk,
Probably because we use pressure coupling and the box size is deformed.
Best regards
Yuguang
Dr. Yuguang Mu
Assistant Professor
School of Biological Sciences
Nanyang Technological University
60 Nanyang Drive Singapore 637551 Tel: +65-63162885 Fax: +65-67913856
http://genome.sbs.ntu.edu.sg/Staff/YGMu/index.php
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Tsjerk Wassenaar
Sent: Wednesday, May 16, 2007 12:49 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] PBC problem
Hi Yuguang,
Warning: Triclinic box is too skewed.
Box (3x3):
Box[0]={ 6.46530e+00, 0.0e+00, 0.0e+00}
Box[1]={ 2.14552e+00, 6.10274e+00, 0.0e+00}
Box[2]={-2.14464e+00, 3.05200e+00, 5.24664e+00}
This is not a rhombic dodecahedron.
CRYST1 64.653 64.689 64.375 70.32 109.46 70.63 P 1 1
This shows that the second vector is larger than the first, thus
violating the gromacs rules for proper boxes (manual chapter 3;
although it could be handled a bit more liberally, especially in the
analysis tools).
Cheers,
Tsjerk
--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before
posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
___
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http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
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