Justin, I have 26 solute atoms and 3302 solvent atoms in my sytems (total 3328 atoms).
1. trjconv -f 3.trr -s 3.tpr -pbc mol -b 400 -e 600 -dt 1 -n 500-1.ndx -o 4-600.xtc here I choose group 0:system (3328 atoms) 2. trjconv -f 4-600.xtc -s 3.tpr -n 500-1.ndx -center -o 4-600-1.xtc For Centering I choose group: solute (26 atoms) For output I choose group : Solvent (3302 atoms) 3. trjconv -f 4-600-1.xtc -s 3.tpr -dump 500 -o 500-11.pdb Here I choose the group: 0 (system). I am geting for error for last command. Fatal error: Index[3302] 3303 is larger than the number of atoms in the trajectory file (3302). It look that there are no solute atoms in trajectory file. Nilesh On Mon, October 17, 2011 7:25 am, Justin A. Lemkul wrote: > > > Nilesh Dhumal wrote: > >> Hello, >> >> >> I have system with solute is surrounded by 256 solvent molecules. I run >> the simulation for 20 ns. I save the snap shot at 500 ps using >> following command. >> >> trjconv -f 3.trr -s 3.tpr -n 500-1.ndx -b 500.0 -e 501.0 -dt 1.0 -pbc >> nojump -center -o 500-11.pdb >> >> I tried to keep the solute at the center box. In visualization, the >> solute is not at center , its close to box edges. >> >> How can I keep the solute at the center. >> >> >> > > You're doing too many things at once. Split the trjconv operation: > > > 1. Run trjconv -pbc mol on the whole trajectory > 2. Run trjconv -center on the output of (1) > 3. Run trjconv -dump 500 on the output of (2) > > > -Justin > > >> I am using Gromacs 4.0.7 version. >> >> >> Thanks >> >> >> Nilesh >> >> >> >> >> >> >> >> >> >> >> > > -- > ======================================== > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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 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 > > > -- 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