Re: Protein Penetrating Water Box

From: salehesam101 . (
Date: Sun Jan 29 2017 - 20:07:08 CST

Hi Oscar,

It seems as though you have "wrapAll" set to "on" on line 62 of the input
file you provided, which is good.

Since you are minimizing and equilibrating your system, I would suggest not
manually defining your PME grid size. Your system should be more flexible
to accommodate for any fluctuations. You should turn on "useflexiblecell"
and "useconstantratio" under the heading "# Constant Pressure Control
(variable volume)".

Please see the pressure control portion of the manual here:

Also, depending on the size of your system, 100 steps for minimization may
not be enough, perhaps consider changing that to ~1000 if you have the cpu

Saleh Al-Khalifa
Villanova University

On Sun, Jan 29, 2017 at 6:25 PM, Oscar Bastidas <>

> Hello Saleh,
> Thank you for your kind response. Attached to this e-mail is a copy of
> the *.CONF input file that I used.
> To answer your question, no, I did not use "wrapAll" variable. I was
> unaware of its existence and use. Would you please tell me under what
> section in the *.CONF file would I place the "wrapAll" variable?
> If you could take a quick look at my *.CONF file just to make sure that
> the other variables are within their acceptable ranges, I would be most
> appreciative. Thank you very much.
> Respectfully submitted,
> Oscar B.
> On Sunday, January 29, 2017, Saleh AlKhalifa <> wrote:
>> Oscar,
>> Can you provide a copy of the input file?
>> When equilibrating, do you use the WrapAll function for PBC?
>> - *wrapAll *[image: $ <$] wrap all coordinates around periodic
>> boundaries? [image: $ >$]
>> *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.
>> Best,
>> 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 *NAME*p_autopsf.psf *NAME*p_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
> --
> Oscar Bastidas, Graduate Student
> Virginia Commonwealth University
> Chemical and Life Science Engineering

Thank you and please have a great day!
Saleh Al-Khalifa
(617) 971-6559

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