[gmx-users] Trouble calculating MSD after removing COM for upper and lower leaflets
Hi All, I have a few older membrane simulations for which the COM for the upper and lower leaflets were not removed in the course of the simulations. These are pretty long simulations exceeding 300 ns. I have trouble with post-processing of the trajectory. To remove the COM of the upper and lower leaflets separately, I executed the following series of commands (shown for upper only): Selecting upper leaflet: g_select -s .tpr -on upper_P8.ndx -select 'resname DPPC and name P8 and res_com z4.3' trjconv -f .gro -s .gro -n upper_P8.ndx -o test_u_P8.pdb .Testing selection, everthing ok Trajectory: trjconv -f .xtc -s .tpr -n upper_P8.ndx -o upperP8_center_pbcnojump.xtc -center -b 2 -pbc nojump MSD: g_msd -f upperP8_center_pbcnojump.xtc -s .tpr -o msd_dppc_x_u.xvg -type x -n upper_P8.ndx Select a group to calculate mean squared displacement for: Group 0 (resname_DPPC_and_name_P8_and_res_com_z4.3_0.000) has 192 elements There is one group in the index Reading frame 60 time 20600.000 Segmentation fault (core dumped) Any ideas? Is there anything wrong with my workflow? Thanks. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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] Trouble calculating MSD after removing COM for upper and lower leaflets
On 11/9/13 5:24 AM, rajat desikan wrote: Hi All, I have a few older membrane simulations for which the COM for the upper and lower leaflets were not removed in the course of the simulations. These are pretty long simulations exceeding 300 ns. I have trouble with post-processing of the trajectory. To remove the COM of the upper and lower leaflets separately, I executed the following series of commands (shown for upper only): Selecting upper leaflet: g_select -s .tpr -on upper_P8.ndx -select 'resname DPPC and name P8 and res_com z4.3' trjconv -f .gro -s .gro -n upper_P8.ndx -o test_u_P8.pdb .Testing selection, everthing ok Trajectory: trjconv -f .xtc -s .tpr -n upper_P8.ndx -o upperP8_center_pbcnojump.xtc -center -b 2 -pbc nojump MSD: g_msd -f upperP8_center_pbcnojump.xtc -s .tpr -o msd_dppc_x_u.xvg -type x -n upper_P8.ndx You probably want the -lateral option as well. Select a group to calculate mean squared displacement for: Group 0 (resname_DPPC_and_name_P8_and_res_com_z4.3_0.000) has 192 elements Does the fact that there are 192 identified P8 atoms match your expectations for this membrane? -Justin There is one group in the index Reading frame 60 time 20600.000 Segmentation fault (core dumped) Any ideas? Is there anything wrong with my workflow? Thanks. -- == 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] Trouble calculating MSD after removing COM for upper and lower leaflets
Hi Justin, 1) I am doing all three. -type x, -type y, -lateral z (xy) ...(I am looking at anisotropy in dynamics if any) 2) Yes, 192 phosphate beads is exact. I have 384 lipids in my system (192/leaflet) If you were to remove the COM motion of individual leaflets and extract the MSD, what would you do? Do you see any error in my workflow? Thanks. Appreciate any suggestions... On Sat, Nov 9, 2013 at 7:16 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/9/13 5:24 AM, rajat desikan wrote: Hi All, I have a few older membrane simulations for which the COM for the upper and lower leaflets were not removed in the course of the simulations. These are pretty long simulations exceeding 300 ns. I have trouble with post-processing of the trajectory. To remove the COM of the upper and lower leaflets separately, I executed the following series of commands (shown for upper only): Selecting upper leaflet: g_select -s .tpr -on upper_P8.ndx -select 'resname DPPC and name P8 and res_com z4.3' trjconv -f .gro -s .gro -n upper_P8.ndx -o test_u_P8.pdb .Testing selection, everthing ok Trajectory: trjconv -f .xtc -s .tpr -n upper_P8.ndx -o upperP8_center_pbcnojump.xtc -center -b 2 -pbc nojump MSD: g_msd -f upperP8_center_pbcnojump.xtc -s .tpr -o msd_dppc_x_u.xvg -type x -n upper_P8.ndx You probably want the -lateral option as well. Select a group to calculate mean squared displacement for: Group 0 (resname_DPPC_and_name_P8_and_res_com_z4.3_0.000) has 192 elements Does the fact that there are 192 identified P8 atoms match your expectations for this membrane? -Justin There is one group in the index Reading frame 60 time 20600.000 Segmentation fault (core dumped) Any ideas? Is there anything wrong with my workflow? Thanks. -- == 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 -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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] Trouble calculating MSD after removing COM for upper and lower leaflets
On 11/9/13 11:37 AM, rajat desikan wrote: Hi Justin, 1) I am doing all three. -type x, -type y, -lateral z (xy) ...(I am looking at anisotropy in dynamics if any) 2) Yes, 192 phosphate beads is exact. I have 384 lipids in my system (192/leaflet) If you were to remove the COM motion of individual leaflets and extract the MSD, what would you do? Do you see any error in my workflow? Thanks. Appreciate any suggestions... What you did looks reasonable to me. Seg faults are frustrating, but can only really be addressed by recompiling in debug mode and running the command through a debugger to see which function is failing. -Justin On Sat, Nov 9, 2013 at 7:16 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/9/13 5:24 AM, rajat desikan wrote: Hi All, I have a few older membrane simulations for which the COM for the upper and lower leaflets were not removed in the course of the simulations. These are pretty long simulations exceeding 300 ns. I have trouble with post-processing of the trajectory. To remove the COM of the upper and lower leaflets separately, I executed the following series of commands (shown for upper only): Selecting upper leaflet: g_select -s .tpr -on upper_P8.ndx -select 'resname DPPC and name P8 and res_com z4.3' trjconv -f .gro -s .gro -n upper_P8.ndx -o test_u_P8.pdb .Testing selection, everthing ok Trajectory: trjconv -f .xtc -s .tpr -n upper_P8.ndx -o upperP8_center_pbcnojump.xtc -center -b 2 -pbc nojump MSD: g_msd -f upperP8_center_pbcnojump.xtc -s .tpr -o msd_dppc_x_u.xvg -type x -n upper_P8.ndx You probably want the -lateral option as well. Select a group to calculate mean squared displacement for: Group 0 (resname_DPPC_and_name_P8_and_res_com_z4.3_0.000) has 192 elements Does the fact that there are 192 identified P8 atoms match your expectations for this membrane? -Justin There is one group in the index Reading frame 60 time 20600.000 Segmentation fault (core dumped) Any ideas? Is there anything wrong with my workflow? Thanks. -- == 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 -- == 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] Trouble calculating MSD after removing COM for upper and lower leaflets
Hi Justin, Thanks for your time. I think I will use g_traj to spit out the P8 coordinates from upperP8_center_pbcnojump.xtc and write my own little MSD routine :) On Sat, Nov 9, 2013 at 11:36 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/9/13 11:37 AM, rajat desikan wrote: Hi Justin, 1) I am doing all three. -type x, -type y, -lateral z (xy) ...(I am looking at anisotropy in dynamics if any) 2) Yes, 192 phosphate beads is exact. I have 384 lipids in my system (192/leaflet) If you were to remove the COM motion of individual leaflets and extract the MSD, what would you do? Do you see any error in my workflow? Thanks. Appreciate any suggestions... What you did looks reasonable to me. Seg faults are frustrating, but can only really be addressed by recompiling in debug mode and running the command through a debugger to see which function is failing. -Justin On Sat, Nov 9, 2013 at 7:16 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/9/13 5:24 AM, rajat desikan wrote: Hi All, I have a few older membrane simulations for which the COM for the upper and lower leaflets were not removed in the course of the simulations. These are pretty long simulations exceeding 300 ns. I have trouble with post-processing of the trajectory. To remove the COM of the upper and lower leaflets separately, I executed the following series of commands (shown for upper only): Selecting upper leaflet: g_select -s .tpr -on upper_P8.ndx -select 'resname DPPC and name P8 and res_com z4.3' trjconv -f .gro -s .gro -n upper_P8.ndx -o test_u_P8.pdb .Testing selection, everthing ok Trajectory: trjconv -f .xtc -s .tpr -n upper_P8.ndx -o upperP8_center_pbcnojump.xtc -center -b 2 -pbc nojump MSD: g_msd -f upperP8_center_pbcnojump.xtc -s .tpr -o msd_dppc_x_u.xvg -type x -n upper_P8.ndx You probably want the -lateral option as well. Select a group to calculate mean squared displacement for: Group 0 (resname_DPPC_and_name_P8_and_res_com_z4.3_0.000) has 192 elements Does the fact that there are 192 identified P8 atoms match your expectations for this membrane? -Justin There is one group in the index Reading frame 60 time 20600.000 Segmentation fault (core dumped) Any ideas? Is there anything wrong with my workflow? Thanks. -- == 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 -- == 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 -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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
