I have run dynamic simulations for kinase protein with gromacs package using gromos force field for 100 ns. At the end of simulations, molecule is out of the box. So how to center the molecule before going for analysis?
Hi Akanksha....
You can use the command as Rajendra kumar suggested " trjconv -f traj.xtc -s topol.tpr -n index.ndx -pbc mol -ur compact -center -o outputfile.xtc", when prompted for groups, for centering use the "protein" and for output use the "system". Upload the output file in VMD you can visualize the whole system. or use the command ( trjconv -f traj.xtc -s topol.tpr -n index.ndx -pbc mol -ur compact -center -o output.gro -dump time ") for dumping the trajectory with single time point (for centering "protein" and for output "system") and upload in VMD, you can observe the protein with in the box.
You have to use trjconv. For example:
trjconv -f traj.xtc -s topol.tpr -n index.ndx -pbc mol -ur compact -center
Then, you will be prompted for two groups, first for centering and second for output. If topology contains more than one chain then use only one chain for centering and whole protein/system (or whatever you want) for output.
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
Hi Akanksha....
You can use the command as Rajendra kumar suggested " trjconv -f traj.xtc -s topol.tpr -n index.ndx -pbc mol -ur compact -center -o outputfile.xtc", when prompted for groups, for centering use the "protein" and for output use the "system". Upload the output file in VMD you can visualize the whole system. or use the command ( trjconv -f traj.xtc -s topol.tpr -n index.ndx -pbc mol -ur compact -center -o output.gro -dump time ") for dumping the trajectory with single time point (for centering "protein" and for output "system") and upload in VMD, you can observe the protein with in the box.
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