Protein Penetrating Water Box

From: Oscar Bastidas (
Date: Sun Jan 29 2017 - 03:15:25 CST


I have recently run a simulation for a total of 600 picoseconds simulated
in a water box. My problem is that when I prepare a pdb file of all
super-imposed snapshots from the dcd file, I notice that two portions of my
protein protrude ever so slightly outside of the water box.

Would someone please tell me if this is a sign of a poorly executed
simulation or are the physics of motion automatically correct and I'm just
simply seeing an artifact anomaly?

Just to be thorough, when I issue the solvate command in Tk Console, I am
presently running the following:

solvate *NAME*p_autopsf.psf *NAME*p_autopsf.pdb -t 5 -o *NAME*_wb

Additional relevant variable values for my present system thus described

restartfreq = 1000
dcdfreq = 5000
xstFreq = 5000
run = 300000

If my simulation is running according to faulty values, could it be the "5"
that needs to be made bigger? Are the above four variables in an
acceptable range of values? Thank you for any help you can provide.


Oscar Bastidas, Graduate Student
Department of Chemical and Life Science Engineering
Virginia Commonwealth University

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