Re: [AMBER] Serious problem at specific time point

From: Jason Swails <>
Date: Wed, 10 Nov 2010 18:53:24 -0500

Hi Hoshin,

My comments are below:

On Wed, Nov 10, 2010 at 3:39 AM, Hoshin Kim <> wrote:

> Dear Amber user,
> I'm trying to do simulation about Enzyme in various solvents, using
> AMBER11.
> But I have a serious problem on my trajectory.
> When I calculated RMSd of catalytic domain of enzyme, slope was suddenly
> soared at 4.8ns (I attached a plotting data). So I ran the VMD to visualize
> what happened at this point, as I attached, protein structure was suddenly
> collapsed at that point !

This is indicative of a corrupt data file. Something has gone awry. My
best guess is that it's an imaging problem. You are not using ioutfm=1, and
you are not using iwrap, so waters are diffusing away, and you're limited by
the size of the numbers in the fixed-format ASCII mdout file. I think what
has happened is one of the numbers has become too large for sander/pmemd to
print in the space allotted to it, so it gives up and fills the field with
*****s. VMD probably comes up to that number, doesn't know what to do with
it, and so moves on to the next one. At this point, your coordinates are 1-
off, leading to what you're seeing here. You can check your trajectory file
for ****s.

If this is the case, either use ioutfm=1 to use netcdf (you should do this,
anyway, since they're better in every way), and/or use iwrap=1. It's only a
matter of time before the same thing happens to your restart file, but it
probably hasn't yet since those fields are larger.

An additional comment below:

> This is my second try. This problem was occurred at almost same point when
> I
> tried to do first simulation using same enzyme, same protocol. So I think
> this error is not the cause of hardware, or something like that
> I'm doing one more simulation using different solvent, It has also same
> problem. (Peak is suddenly increased at specific time-steps) only
> difference
> is time point.
> Could anyone figure out this serious problem?
> Thanks in advance,
> Hoshin Kim,
> P.S.
> 1.Attached files are only about the problem which I explained first.
> 2.First case, solvent is 0.3M NaCl solution, Second case, [Bmim][TfO]
> 3.I am using enzyme named 1TCA (CalB), and protocol for production MD is as
> follows,
> -------------------------------------------------------------
> imin=0,
> ntxo=1, ntrx=1,
> cut=9.0, tempi=300.0, ntwprt=0,
> ntpr=500, ntwx=500, ntwe=500, ntwr=500,
> nstlim=10000000, temp0=300.0,
> dt=0.002, nscm=100,nsnb=10,dielc=1.0,
> ntc=2, ntf=2, tol=0.00001,
> ntx=5, irest=1, heat=0.0,
> ntb=2, ntp=1, pres0=1.0, taup=0.5,
> scee=1.2, dt=0.002,

The presence of scee is slightly disturbing to me... SCEE was removed from
the &cntrl namelist and incorporated into the prmtop file for Amber11. Are
you sure you're using the up-to-date Amber11 release with all the bug fixes?

All the best,

  ntt=1, vlimit=20.0,comp=44.6,
> ig=71277,
> &end
> -----------------------------------------------------
> If further protocols are need to figure out this problem (Protocols for
> minimization, equilibration ...), please tell me !
> ----------------------------------------------------------------------------
> -------
> Hoshin Kim
> Now)
> Visiting Scholar
> Department of Chemical and Biomolecular Engineering
> North Carolina State University
> Raleigh, NC 27695
> Phone: 919-986-9258
> Also)
> Graduate student (M.D. candidate)
> Ionic Liquids Team(ILs) in Bio Nano Process Lab
> Department of Biological Engineering,
> 2S 113, Engineering building Inha University,
> 253 Yonghyeon Dong, Nam Ku
> Incheon, KOREA
> TEL) +82-32-860-8655
> ----------------------------------------------------------------------------
> -------
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Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Wed Nov 10 2010 - 16:00:04 PST
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