AMBER Archive (2006)

Subject: Re: AMBER: Failure of iwrap in PMEMD

From: Myunggi Yi (myunggi_at_gmail.com)
Date: Thu Jul 20 2006 - 10:04:31 CDT

Thank you all,

Dr. Duke,

I have never seen this before using sander.
This system is not big, and as you see this is only the equilbration step.
I saw this less than 500 ps short simulation.
For the big system size and long time simulation, I have to use iwrap.
As you know, the coordinate larger than 999.999 can't be formatted out,
and the program crashs.

I will send you my trajectory, topparm, and input/output files.
By displaying with VMD, you will see the waters outside the primary
unit cell (orthogonal).

Have a nice day.

On 7/20/06, Robert Duke <rduke_at_email.unc.edu> wrote:
> 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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>
>
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-- 
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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