Hello All,
I have a question regarding the usage of gmx select. I want to select water molecules in a particular subset in z-direction (example z > 5 and z < 10) for each frame of my trajectory and then carry out analysis using g_mindist on each frame of the trajectory (with selections) For example: system consists of peptide 1 and peptide2, membrane, water and ions. using g_mindist, I want to calculate the number of contacts peptide1 is making with water vs. peptide2 in z >5 and z < 10 over the whole trajectory. When I try to make selection using: The option pdbatoms selected only lists the selected atoms. The option pdbatoms all lists everything. The -on options gives me the index file of only selected atoms: gmx_mpi select -f 432000g1.gro -s ../../3run_npt_noposre.tpr -select '(resname TIP3 and name OH2) and z > -10 and z < 20' -oi -pdbatoms selected -on insel.ndx I am a little confused how to incoporate the slections in odere to carry out the analysis I am interested in. Kindly suggest. Thanks for your time in advance. Regards, sn -- 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.
