Re: Protein Penetrating Water Box

From: Saleh AlKhalifa (
Date: Sun Jan 29 2017 - 14:02:05 CST


Can you provide a copy of the input file?
When equilibrating, do you use the WrapAll function for PBC?

wrapAll wrap all coordinates around periodic boundaries?
Acceptable Values: on or off
Default Value: off
Description: Coordinates are normally output relative to the way they were read in. Hence, if part of a molecule crosses a periodic boundary it is not translated to the other side of the cell on output. This option alters this behavior for all contiguous clusters of bonded atoms.

Saleh Al-Khalifa
Villanova University

> On Jan 29, 2017, at 04:15, Oscar Bastidas <> wrote:
> Hello,
> 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 NAMEp_autopsf.psf NAMEp_autopsf.pdb -t 5 -o NAME_wb
> Additional relevant variable values for my present system thus described are:
> 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.
> Regards,
> Oscar Bastidas, Graduate Student
> Department of Chemical and Life Science Engineering
> Virginia Commonwealth University

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