AMBER Archive (2006)

Subject: Re: AMBER: Failure of iwrap in PMEMD

From: darden (darden_at_gamera.niehs.nih.gov)
Date: Thu Jul 20 2006 - 09:34:47 CDT

dear MYUNGGI
first of all, you likely have nothing to worry about with respect to the
validity of the simulation. both pmemd and sander do the wrapping
internally when it comes to calculating energies. that is, the water is
imaged (inside the program) back into the box for purposes of vdw and
electrostatic energies, whether or not you see it leave the box.

the reason to let the waters wander (or any other molecule) using iwrap
options is that often it is much easier to do analyses on the unwrapped
trajectories. however sometimes this causes problems, hence there are
options for the trajectory output

as far as the details of how pmemd handles iwrap--bob duke is better
qualified to handle that
hope this helps
tom darden
On Thu, 20 Jul 2006, Myunggi Yi wrote:

> Dear Amber users,
>
> I found the failure of image control (iwrap) in PMEMD (amber8).
> As time goes by, more and more water molecules came out of
> the primary box in my simulation.
>
> I have never seen this before using SANDER (iwrap).
> The following is my input, and I haven't found any error,
> warning, and weired thing in the output file.
>
> ==========================
> npt eq
> &cntrl
> nstlim = 1000000, dt=.002,
> irest=1, ntpr=500, ntwx=500, ntx=5,
> temp0=310.0, ntt=1,
> tautp=2.0, taup=2.0, cut=9.0,
> ntb=2, ntp=2, iwrap=1,
> ntc=2, ntf=2,
> /
> ==========================
>
> I know this won't effect the simulation, and
> I can handle this using ptraj in the post analysis.
>
> Is there anything wrong in my input?
>
>
> --
> Best wishes,
>
> MYUNGGI YI
> ==================================
> KLB 419
> Institute of Molecular Biophysics
> Florida State University
> Tallahassee, FL 32306
>
> Office: (850) 645-1334
> http://www.scs.fsu.edu/~myunggi
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