From: Ashar Malik (
Date: Sat Oct 23 2021 - 00:42:39 CDT

Hi Ryan

Again not familiar with the contents of the string above and how each of
the values is being used.
I am also not familiar with how you set up your system.

Taking your system as an example a typical workflow will look
something like this

A membrane + protein system is constructed which is then minimized followed
by solvation/ionization, minimized again and then the system goes into MD.

At each step when things are being moved or added your system size can

Just before MD, you have to know the system size. The way I am familiar
with MD is through the use of a config file which contains line-by-line a
collection of variables that you can change the value of. Programs like
NAMD will then read that list and the explicit values from the config file
will replace system defaults. Some values have no defaults and must be

e.g., see here

Within the description listed in the page above you will notice 4 lines.

# Periodic Boundary conditions
cellBasisVector1 dx 0. 0. ;# vector to the next image
cellBasisVector2 0. dy 0.
cellBasisVector3 0. 0 dz
cellOrigin 0. 0. 0. ;# the *center* of the cell

I have substituted the values to dx, dy, dz for generalization.
Your system size before MD (i.e. length along x, y and z axis) needs
to be plugged into dx, dy and dz.
cell Origin will point to the centre of the box which can be 0, 0, 0
if it's at origin.

This now controls the boundaries across which the wrapping will take
place. If your system is larger and the boundaries you choose are
smaller then I suspect that you will get the behaviour you see.
Disclaimer: I have never seen this in my work, but I suspect that the
above might be the reason.

So I believe my boundaries are "145.078088","145.078088","144.858064" and
> compared to your calculations of 180 188 158 these do not match up, correct?
If the values are used as boundaries for your entire system (i.e.,
membrane + water) and the minmax result you provided earlier - then yes.
Your periodic setup is smaller than your entire system which can explain
why your "jumps" appear with the system instead of on edges.

> For clarification, the charmm-gui of 135-145 is the approximate x,y,z
> dimensions you give Charmm-gui to create a system for you. So each system I
> have (9 of them) I used the input range from 135-145 angs depending on the
> system. For this system I'm using as an example I think I used 145 but
> there are others that are around 135. Sorry for the confusion, I think this
> is irrelevant information and whatever we fix in this system I can apply to
> the others.

Does this mean that 145 is your size in x, y and z?
Also - are you sure this (145) is the size of your entire system?
Membrane + protein + waters?

> Apologies for being new to this.

We all start from somewhere.

Hopefully the above explanation will clarify things.