AMBER Archive (2006)

Subject: Re: AMBER: Failure of iwrap in PMEMD

From: Myunggi Yi (myunggi_at_gmail.com)
Date: Thu Jul 20 2006 - 19:24:34 CDT

Dear Dr. Duke,

As you see, my system is solvated DMPC bilayers with a drug molecule.
I did exactly same simulation with sander, and I have some experience also.
I'm sorry for not sending you my trajectory.
The file is big. I couldn't attach it.

If you run with PMEMD with the restart file and input (iwrap=1) file
(I did with IBM SP4 with 8cpu's),
you will see some water molecules out of the unit cell (about after 500ps).
Compare with the sander (iwrap=1) result.
I know I see some part of the lipid chain outside the box, but not
whole lesidue.
However, I saw several water molecules (one lesidue) outside the box.
I have never seen like this before using sander.

I will try to send my trajectory to you later.

Thank you and have a nice day.

On 7/20/06, Robert Duke <rduke_at_email.unc.edu> wrote:
> Myunggi -
> Okay, I have looked at this. Your system has got several thousand waters
> with several thousand residues of some sort, looks like roughly 13C
> aliphatic, with several oxygens, all individual molecules, in a band in the
> middle of the simulation cell. In a sense there is no solute; just a couple
> of different solvents with significantly different polar character. I noted
> 1 other small molecule in there somewhere. The restart file looks "in the
> box" to me looking at vmd, and it is a 50 psec snapshot I think. Now, for a
> molecule to be wrapped by the wrapping routine, it's geometric center has to
> go outside the box. This means for the aliphatic stuff, you will see half
> chains waving around outside the box. I don't know where the actual box
> boundaries are, but generally the edges look more dilute because you are not
> looking through as much solvent. So I did two 100 psec runs with pmemd 8,
> one with iwrap off, and one with iwrap on. I took 50 trajectory snapshots
> over the 100 psec. What I see when iwrap is off is that the water does
> diffuse out, but the hydrocarbon stuff does not; the visual effect is of a
> dogbone where the ends are growing, if you know what I mean. With iwrap on,
> what I see is all the molecules retained in the simulation cell, though the
> long carbon chains are more visible for the molecules that are less than
> half "out of the box". Now, if it takes a longer simulation, fine, but why
> don't you send me the mdcrd you have rather than me doing a 0.5 nsec run
> just to reproduce this. Looking at the code, I don't see how there would be
> a problem, but this simulation is not the usual case, so maybe something
> else strange is going on. When you say that you have not seen problems with
> sander, have you run this exact system with sander? My bet is sander would
> do the same thing, since the code is pretty much the same, but I don't yet
> see a problem with pmemd.
> Regards - Bob Duke
>
> ----- Original Message -----
> From: "Myunggi Yi" <myunggi_at_gmail.com>
> To: <amber_at_scripps.edu>
> Sent: Thursday, July 20, 2006 11:04 AM
> Subject: Re: AMBER: Failure of iwrap in PMEMD
>
>
> > 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
> >> > -----------------------------------------------------------------------
> >> > The AMBER Mail Reflector
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> >> > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> >> >
> >>
> >>
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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
> > -----------------------------------------------------------------------
> > The AMBER Mail Reflector
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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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