AMBER Archive (2006)

Subject: Re: AMBER: Failure of iwrap in PMEMD

From: Robert Duke (rduke_at_email.unc.edu)
Date: Thu Jul 20 2006 - 09:40:48 CDT

Myunggi -
I am not aware of any problem with the code, and see no problem with your
input. What type of unit cell are we dealing with here (orthogonal vs.
truncated octahedron)? Anything else wierd at all? The pmemd wrapping code
is pretty much the same as the sander wrapping code I believe, but will have
to check. Are you sure that you would not see the same thing if you ran for
as long in sander? If you send me inputs/outputs (a small number of
trajectory frames for output, of course) I will take a further look. I
believe a lot of folks do wrapping primarily with ptraj these days. I have
seen examples of strange simulations where even the restrt file format was
overflowed by parts of the simulation being strongly repelled, but when that
happens you obviously have something wrong going on. Is this a system that
has been simulated for a really really long time by any chance?
Regards - Bob Duke

----- Original Message -----
From: "Myunggi Yi" <myunggi_at_gmail.com>
To: <amber_at_scripps.edu>
Sent: Thursday, July 20, 2006 10:01 AM
Subject: AMBER: Failure of iwrap in PMEMD

> 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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