I have a dimer protein with its crystal structure available. I have performed MD simulation for the same for 100 ns. While performing RMSD analysis, the plot that I have got looks unusual inferring to protein moving out of the box.
I tried to re center the protein by using the following command: gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -center, but it didn’t change the rmsd plot.
Thank you for your response.
Yes I did check the posts on the forum discussing the same problem and tried using same commands. But somehow, the RMSD plot didnot get any better.
The reference file I am using with -s is md_0_1.tpr, can I use any other .tpr or .gro file for centering my protein?
tpr file is a binary file. you can dump the pdb file from the tpr. To find the RMSD, you need the crystal structure as a pdb file. If crystal structure is not present then an average structure(from your trajectory) can be used as a reference structure.
Take a look at the post I made a while ago at the 3rd party tools section of this forum. mdvwhole will solve your problem and you do not need to fiddle with your trajectory. I do not know how you solvent is named, but after installing (takes a while as I did not clean the dependencies yet…) you should run the following command replacing WATER and IONS with their respective residue names in your system: