AMBER Archive (2006)

Subject: Re: AMBER: Failure of iwrap in PMEMD

From: Myunggi Yi (myunggi_at_gmail.com)
Date: Fri Jul 21 2006 - 08:57:03 CDT

Thank you.

As I and you have mentioned, one will have the trajectory format problem
when he/she run a long MD simulation with a big box (system).
If you don't use iwrap during MD run, you will see ******* instead of
coordinates.
Then you have to rerun your MD using the previous restart file
(after doing center and image with ptraj).
Of course, you lose the current trajectory.

Have a nice day.

On 7/21/06, Robert Duke <rduke_at_email.unc.edu> wrote:
> Hi Myunggi -
> Okay, I did a 0.5 nsec simulation overnight on 4 pentiums, amber 8, and
> basically confirmed what you are saying. I looked at the wrapping code. It
> is identical to the amber 6 sander wrapping code. In amber 7 the sander
> code was changed without explanation; I thought it was a performance issue
> (and I have not been that worried about wrapping performance, so I did not
> track the change). So there may be a hole in the wrapping algorithm. An
> important point here is that this in no way affects the validity of results
> from pmemd - wrapping is only a visulization aid and is only done to the
> mdcrd trajectory, not to any internal data. So this simply means that
> currently to get a clean trajectory for visualization, you need to go
> through ptraj (which apparently most people do anyway instead of using
> iwrap - it is more efficient to wrap on one processor rather than having a
> roomful of cpu's waiting for the master to do the wrapping, and wrapping is
> not a parallelized process at the moment). I will check this out further
> and issue fixes for amber 8 and 9 (I will probably just end up adopting the
> new code). So there is no need to send your trajectory. And there is no
> need for anyone to worry about their results. Thanks for pointing this out,
> though.
> Best Regards - Bob
>
> ----- Original Message -----
> From: "Myunggi Yi" <myunggi_at_gmail.com>
> To: <amber_at_scripps.edu>
> Sent: Thursday, July 20, 2006 8:24 PM
> Subject: Re: AMBER: Failure of iwrap in PMEMD
>
>
> > 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
> >> >> > -----------------------------------------------------------------------
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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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> >>
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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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-- 
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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