I have done MD simulation of DNA alone and complex, but the rmsd of the complex is much greater than alone DNA. What could be the possible reason for this?
i have give centring command before calculating rmsd-
gmx trjconv -s *.tpr -f *.xtc -o *_center.xtc -center -pbc mol -ur compact
gmx trjconv -s *.tpr -f *.xtc -o *_noPBC.xtc -pbc mol -center
Hello
Please read this short tutorial about RMSD
http://www.mdtutorials.com/gmx/lysozyme/09_analysis.html
You have to use the trjconv tool obtain the .xtc file (trajectory) corrected for any periodicity and then run the analysis.
🌾
@Rezvan Marjani i have goven trjconv command as i mention it previously but it still gives high rmsd.
I would suggest you visualize the trajectories. It mostly dues to you do not remove PBC properly, especially for the multi-molecules system
@Quyen V. Vu i have done visualisation as the complex come at the corner of box . I am trying to remove pbc but it is not working.
Remove PBC for the multi-molecules system is quite tricky, try to combine different options available for gmx trjconv to obtain your goals
Cheers,
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