I have followed the "Tutorial for Trypsin-‐Benzamidine complex molecular dynamics
study" (pdf file attached below) and some of the inputs i have changed according to my protein name and ligand name.
I am getting a huge fluctuations in RMSD and it looks like my protein was not stable.
Please help me with this and I don't know where i made a mistake.
All .mdp files were taken from bevan's lab tutorial.
It seems normal. The "apparent" mistake is due to the fact that you have not considered the artifacts introduced by the periodic boundary conditions. Prior to perform any further analysis you must re-sample you raw trajectory (for instance using "trjcov" command with "-pbc nojump" option).
It seems normal. The "apparent" mistake is due to the fact that you have not considered the artifacts introduced by the periodic boundary conditions. Prior to perform any further analysis you must re-sample you raw trajectory (for instance using "trjcov" command with "-pbc nojump" option).
Dear Dario Corrada,
Thank you for your reply. But during analysis I had given the following command. Using that command I got that result. (image attached above).
trjconv –s md.tpr –f md.trr –o md.xtc –pbc nojump
My suggestion is only one of alternative solutions for PBC artifact correction. If you read the help about trjconv command you will find other additional strategies to try.
Good luck
Please try " -pbc atom -ur compact -center" and in index.ndx create an entry of a single heavy atom.
Dear Mandar Kulkarni,
Thank you so much for your reply. The command works and I got a good Graph.
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