I am running a 10 ns NVT production run MD simulation of a protein in NAMD. Everything looked fine till 9 ns, but during the end of the simulation, while running the dcd in VMD, it seems like the protein is trying to come out of the water box. I don't know what's the issue in here since I think I have set everything fine in the conf file. Will this effect my simulation ? and how can I fix this issue of my peptide coming out of the box ?
Thanks
Its fine. Remember that you are using periodic boundary conditions for your simulation. After loading the psf and dcd files, in VMD command window type: pbc wrap -centersel "protein" -center com -compound residue -all
Thank you sir. But, the command you suggested me to use in vmd fetched this error: Suspicious pbc side length (a=0.000000 b=0.000000 c=0.000000). Have you forgotten to set the pbc parameters?
domain error: argument not in valid range
Please do not load the pdb file. Only load the psf and dcd files. If you keep getting the error message then that means you have to rerun your simulation with periodic boundary conditions.
Thanks sir. It worked, but a strange problem is showing up which I have attached here with. The protein looks like a bit stretched towards the middle and the end of the simulation after using this command. Why is this showing up ? Thanks
See if changing the 'compound' flag helps. Something like:
pbc wrap -compound fragment -center com -centersel "protein" -all
Thanks Aditi. The distortion of the protein no longer occurs, but it seems the arrangement of the water molecules breaks a bit towards the end of the simulation when I use this command.
Does shifting the centre of the water box with "-shiftcenter {x y z}" do anything?
For example, a command like:
pbc wrap -compound fragment -center com -centersel "protein" -all -shiftcenter {0 1 0}
Thanks Aditi. Now, my protein fits perfectly inside the water box during the simulation. So, what was the issue earlier and how this command fixed it ? Can you please explain a bit. Thanks
I am so happy to know that worked!
As far as I understand, during simulations using PBC, the system can move out of the box from one face (only to re-enter from the opposite face). However, we don't get to see that, we just see the system moving out of the box into nothingness. To fix this, we need to wrap the coordinates of the system, which brings it back into the box, so that we can visualise the system in it's entirety.
Sometimes wrapping can split a compound (the protein here) by wrapping it's atoms around the periodic box. This creates the distortions you saw. The "compound" flag is used to tell VMD which compound it should not split by wrapping. The command "-compound" specifies the atom compounds which must be kept together and not wrapped in case their wrapping should split that compound. Sometimes we need to mention this, so that the wrapping does not end up distorting the system.
You can find more about PBC commands here:
http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/
http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/
Make sure that the beta value of the central ligand must be 1 in the pdb file. Then, I hope this problem wont come again.
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