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 z>4.3' >>>> 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 20000 -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_z>4.3_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 list gmx-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 list gmx-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 list gmx-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
