[gmx-users] VMD visualization is failed

mary ko maryko2019 at yahoo.com
Thu Mar 7 18:12:10 CET 2019

Dear all
I have simulated a protein-ligand system and the md.xtc and md.gro are now generated in the output. Unlike my previous simulations of nano systems in which the .trr trajectory was in the output and the visualization could be done in an straight forward way of opening the .gro and .trr consecutively, the .trr is not present now. I used gmx_mpi -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o md.tpr AND gmx_mpi mdrun -ntomp 2 -pin auto -s md.tpr -cpi md.cpt -tunepme -v -gpu_id 0 -nb gpu AND also gmx_mpi trjconv -f md.xtc -s md.tpr -o md_convert.gro -ur compact -pbc mol -center. How should I visualize the simulation in VMD having the .gro and .xtc?Is there a problem in the commands I used or a missing option in the .mdp that the .trr is not generated?Thanks.

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