AMBER Archive (2006)

Subject: Re: AMBER: Failure of iwrap in PMEMD

From: Robert Duke (rduke_at_email.unc.edu)
Date: Thu Jul 20 2006 - 16:35:58 CDT

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
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
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