Hello,
I performed 100ns protein - ligand MD simulation using gromacs. When I calculate the RMSD I see weird jump at 60ns. I used no jump and center to create nopbc.xtc file also used fit + rot options. But still the problem remains. Could any body help to solve the issue.
Thank you,
nitin
It may not be the PBC. It may just be a part of your protein starting to be more dynamic - Loop dynamics? Loss of secondary structure somewhere? Visualize your centered trajectory from 70 to 90ns. It might make it easier for you to spot the perturbation if you align your protein backbone to a reference throughout the trajectory (try RMSD trajectory tool in VMD?).
Thank you for the reply I visualized the trajectory in VMD using .gro file from gromacs. I saw that some part of protein was outside (see pic1.png). I used pbc command in VMD (pbc wrap -centersel "protein" -center com -compound residue -all). After this protein was centered (see centered.png). Now the question is how do I export this to .gro file and perform RMSD analysis using gmx rms command in gromacs.
Dear Sainitin Donakonda
Please check 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.
Hi Sainitin Donakonda
Good to hear you found the PBC issue. I'm not sure about exporting trajectories from VMD but here's how you can do the centering and RMSD analysis in gromacs:
gmx trjconv -f input.xtc -s input.tpr -o centered.xtc -pbc mol -center -boxcenter tric -n index.ndx
(if your protein starts in the center from the beginning of the simulation, then you can select 'Protein' when prompted. Otherwise, just to be safe, select a single C-alpha atom toward the center of the protein. Use gmx make_ndx to make the C-alpha atom selection in the index.ndx file)
Then,
gmx rms -f centered.xtc -s input.tpr -o RMSD.xvg
(select C-alpha atoms when prompted)
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