RMSF AND ngmx in GROMACS

Question

[adammbbs]

HI

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?

Answer 1

[dasdevashishdas]

1. 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 )

1. 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

http://manual.gromacs.org/programs/gmx-rmsf.html