Re: Functionality of wrapWater and wrapAll commands for periodic simulations

From: Harish Srinivasan (harishlglk1992_at_gmail.com)
Date: Wed Mar 07 2018 - 23:11:19 CST

Hi Giacomo,

Therefore, if I set *wrapAll on*, will my simulation DCD trajectories
produce wrapped positions or unwrapped ones?

Indeed it is the transformation to the gel phase, but the concern really is
that at 350 K, it is supposed to remain in the fluid phase (which it
initially did before for the first 20 ns before I restarted the run).
Thank you for clarifying about the part on earlier versions of CHARMM
forcefields. But just to be clear, are you saying this is the kind problem
observed in the earlier versions of CHARMM forcefields?

I am using CHARMM36 forcefields only, except for one or two dihedrals which
were not available in CHARMM36, so they're generated from the cgenff.

Thank you
Harish

On 7 March 2018 at 19:05, Giacomo Fiorin <giacomo.fiorin_at_gmail.com> wrote:

> 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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