I am working on simulation of some compounds that were identified from a virtual screen. This is one particular example wherein I am observing the spikes in the RMSD values plot over the course of the simulation. I have attached the file for the reference.
Is this because the ligand is charged in this case?
All other complexes do not show the spikes in between.
I would like to know if any one has experienced this before and how to justify this.
May i have a question: how does Schrodinger calculate the concentration of sodium (0.06M) and chloride ions (0.05M), from the volume of the simulated box?
Shouldn't the concentration of ions be calculated based on the ratio between number of ions and number of water molecules?
Sodium ions: 55.5 * 34/10355 = 0.18 M
Chloride ions: 55.5 * 29/10355 = 0.16 M
Just a thought here, is your simulation box big enough for the protein of interest? If you're running using Desmond's defaults (judging from the number of atoms) the box is 10 A, perhaps the initial portion of the protein is interacting with itself.
Even if you don't see such behaviour in other simulations double check this.
Regards
Hi heena
As Wojciech Kopec previously stated, the most common problem of spike appearance in a simulation comes from the protein crossing periodic boundaries. When faced with this problem I process my journey with this script in VMD (I use NAMD for MD simulations):
package requires pbctools
new mol.psf file
mol addfile file.dcd wait for everyone
pbc wrap -centersel "segname R" -center com -compound remainder -all
animate write dcd file_out.dcd
Departure
The script centers the protein and prevents it from reaching the limits of the water box.
I hope I have been helpful
Greetings
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