Functionality of wrapWater and wrapAll commands for periodic simulations

From: Harish Srinivasan (harishlglk1992_at_gmail.com)
Date: Wed Mar 07 2018 - 05:34:08 CST

Dear all,

I am running a simulation of a lipid bilayer in water under periodic
boundary conditions in 3D. I am using

*wrapAll off*
*wrapWater off*

in the configuration file.

I hope the simulation still continues with periodic boundary conditions
intact. If that is the case, what do the above commands affect? Do they
affect DCD trajectory or it has no bearing on it?

Moreover, when I am using the restart file to start the next run. It also
has no PBC applied to it. I believe this is because of the above commands.
Should this be problem when I am restarting runs (I include the restart xsc
file along with coor and vel files)?

Thank you
Harish

*PS*: I am getting some weird results after using restart files! The
bilayer system which was significantly disordered (gauche conformations in
the alkyl chains of the bilayer) in the restart file (of say 350 K run),
started getting ordered automatically despite maintaining the simulation
temperature (at 350 K) using a Langevin piston technique.

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