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How to check and visualise the box dimension at protein ligand simulation in GROMACS 5.0.4 ?
What is the command for getting RMSF graph in GROMACS 5.0.4?
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adammbbs •
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- How to check and visualise the box dimension at protein ligand simulation in GROMACS 5.0.4 ?
It depends on which format (PDB, GRO and XTC) you want to use.
For visualization:
Use VMD ( www.ks.uiuc.edu/Research/vmd , http://www.gromacs.org/Developer_Zone/Programming_Guide/VMD).
To check:
Please check the Gromacs log file for box size (http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/Topology_preparation%2C_%22What's_in_a_log_file%22%2C_basic_performance_improvements%3A_Mark_Abraham%2C_Session_1A )
- what is the command for getting RMSF graph in GROMACS 5.0.4?
gmx rmsf -s [TPR File] -f [XTC_File] -o [Output_XVG_file]
e.g.
gmx rmsf -s md.tpr -f md.xtc -o output.xvg
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