Re: Functionality of wrapWater and wrapAll commands for periodic simulations

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Wed Mar 07 2018 - 07:35:30 CST

Hi Harish, PBCs are always on if you are defining them in the config file.
The convention used for wrapping has no effect on the physical trajectory,
due to periodicity. Wrapped and unwrapped positions may not be the same,
but velocities and forces surely don't change.

As for the bilayer simulation, that sounds like a gel transition: check the
lipid force field you are using. Older version of CHARMM had this very
problem, and knowledge of this used to be well known among practitioners
but since it wasn't mentioned much in the literature we tend to forget
about this issue after CHARMM 36.

Giacomo

On Wed, Mar 7, 2018 at 6:34 AM, Harish Srinivasan <harishlglk1992_at_gmail.com>
wrote:

> 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.
>

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin

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