Yes, sorry, my bad... Running on autopilot.
All the best
Ross
> -----Original Message-----
> From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On
> Behalf Of aapeters.ncsu.edu
> Sent: Thursday, April 29, 2010 4:59 AM
> To: amber.ambermd.org
> Subject: RE: [AMBER] QM/MM cut problem
>
>
> Hi Ross
>
> Instead of "patch -p0 <bugfix.all"
> you mean "patch -p0 <bugfix.35" right?
>
> Andrew
>
> > Hi Andrew,
> >
> > Can you try applying the attached bugfix.35 to your AMBER 10 and see
> if it
> > fixes your problem. Make sure you first apply bugfix.all and then
> copy
> > bugfix.35 to $AMBERHOME/src/sander/ and
> >
> > patch -p0 <bugfix.all
> >
> > Recompile and run the tests and then try it with your system. I think
> this
> > should address the problem. It shifts the QM region by the center of
> > coordinates of the QM atoms rather than just shifting the first QM
> atom to
> > be at the origin. I have not had time to rigorously test this though
> so if
> > you could try it with several different QM setups it would be really
> > helpful.
> >
> > All the best
> > Ross
> >
> >> -----Original Message-----
> >> From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org]
> On
> >> Behalf Of aapeters.ncsu.edu
> >> Sent: Tuesday, April 20, 2010 11:28 AM
> >> To: AMBER Mailing List
> >> Subject: RE: [AMBER] QM/MM cut problem
> >>
> >>
> >> Hi Ross
> >>
> >> Thanks for your response. The junk in my input file is evolutionary
> >> leftovers from previous runs. I used a small system and a small
> cutoff
> >> because I'm trying to hone in on the problem. I have done several
> >> dozens
> >> of picoseconds of qmmm with this system, gradually ramping up from
> 0K
> >> to
> >> 16K at constant pressure. So I don't think that the evolutionary
> >> leftovers in the input file are causing the problem.
> >>
> >> I want to draw your attention to the following:
> >>
> >> According to the attached output file (and the qm_region.pdb file),
> the
> >> min and max Z are -5.884 and 5.884, which gives a size of 11.76. So
> >> the z
> >> size + 2*cutoff is 19.76Ang. But then later in the same output
> file,
> >> it
> >> says the QM Z size is 29.962Ang. Isn't this a conflict? The system
> >> only
> >> moved one step. I set it up this way to hone in on the problem.
> >>
> >>
> >> Andrew
> >>
> >>
> >>
> >> > Hi Andrew,
> >> >
> >> > The bounds for QMMM calculations are slightly different than the
> >> bounds
> >> > for
> >> > regular MM calculations. The MM pairlist is separate for each
> atom.
> >> Thus
> >> > with an 8A cutoff each atom is surrounded by a sphere of 8
> angstroms
> >> > radius
> >> > which should not extend across two boxes. For the QM region, for
> >> stability
> >> > reasons since having different charges in the Fock matrix for
> >> different QM
> >> > atoms can cause problems, each atom shares the same non-bond list.
> >> Thus
> >> > each
> >> > QM atom interacts with MM atoms that are within qmcut of ANY QM
> atom.
> >> This
> >> > means that your QM region is effectively surrounded by a MM region
> of
> >> size
> >> > QMcut. In order to not violate the minimum image convention this
> >> means
> >> > that
> >> > your box must be at least the largest dimension of the QM region +
> >> the
> >> > cutoff.
> >> >
> >> > This should be what the message below is telling you. Your box can
> >> contain
> >> > a
> >> > sphere of 11.146 angstroms radius But the QM dimensions plus the
> >> cutoff
> >> > are
> >> > larger than this. Solution = use a much larger water box.
> >> >
> >> > With regards to the difference in the absolute values of the
> bounding
> >> box:
> >> >
> >> > ERROR: QM region + cutoff larger than box dimension:
> >> > QM-MM Cutoff = 4.0000
> >> > Coord Lower Upper Size Radius of largest sphere
> inside
> >> unit
> >> > cell
> >> > X -5.632 13.150 18.782 11.146
> >> > Y -5.431 13.671 19.102 11.146
> >> > Z -15.168 14.794 29.962 11.146
> >> >
> >> > One needs to consider the coordinates to simply be relative here.
> For
> >> > simplicity inside the QM routines the QM region is extracted from
> the
> >> > main,
> >> > unimaged, coordinate array. It is then imaged and centered. Then
> the
> >> MM
> >> > atoms that fall within the cutoff are also rebased to be within
> the
> >> QM
> >> > calculations central QM region origin setup. Hence the coordinates
> >> written
> >> > from within the QM region will not have the same origin as the
> inpcrd
> >> > file.
> >> >
> >> > Note, looking at your system:
> >> >
> >> > 1) NATOM = 1280
> >> >
> >> > This is VERY small, especially since you have some 160 QM atoms.
> >> Likely
> >> > you
> >> > have nowhere near enough water.
> >> >
> >> > 2) cut=4.0
> >> >
> >> > I assume you just made this smaller in order to see if you could
> get
> >> the
> >> > calculation to run, rather than actually intending to run
> simulations
> >> with
> >> > a
> >> > 4 angstrom cutoff. This should NEVER be reduced below 8.0. In fact
> I
> >> vouch
> >> > that the sander code be modified to refuse to run with cutoffs of
> >> less
> >> > than
> >> > 8.0.
> >> >
> >> > 3) Your mdin file appears to be full of lots of junk and strange
> >> settings.
> >> >
> >> > imin=0, maxcyc =1000,
> >> >
> >> > You specify maxcyc even though imin=0. This just leads to
> confusion.
> >> > You set tempi=1.0 even though you have irest=1. Again just
> confusion.
> >> > You specify tautp=0.1 even though you have ntt=3 which does not
> use
> >> tautp.
> >> > temp0=16.0 = You really want to run at just 16K? Scaling from 14
> >> kelvin to
> >> > 16 kelvin over 2000 steps?
> >> > You try to do NTP (ntb=2,ntp=1) at VERY low temperature. Use of
> >> constant
> >> > pressure at low temperatures will undoubtedly lead to
> instabilities.
> >> > You set offset=0.09 but are running PME. Again confusing.
> >> > You set clambda even though you are not running thermodynamic
> >> integration.
> >> >
> >> > Good luck,
> >> > Ross
> >> >
> >> > /\
> >> > \/
> >> > |\oss Walker
> >> >
> >> > | Assistant Research Professor |
> >> > | San Diego Supercomputer Center |
> >> > | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> >> > | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
> >> >
> >> > Note: Electronic Mail is not secure, has no guarantee of delivery,
> >> may not
> >> > be read every day, and should not be used for urgent or sensitive
> >> issues.
> >> >
> >> >
> >> >
> >> >
> >> >
> >> >
> >> >
> >> >
> >> >> -----Original Message-----
> >> >> From: amber-bounces.ambermd.org [mailto:amber-
> bounces.ambermd.org]
> >> On
> >> >> Behalf Of aapeters.ncsu.edu
> >> >> Sent: Tuesday, April 20, 2010 9:36 AM
> >> >> To: amber.ambermd.org
> >> >> Subject: [AMBER] QM/MM cut problem
> >> >>
> >> >> Hello users
> >> >>
> >> >> When using Amber10 QM/MM I get errors complaining my box is too
> >> small.
> >> >>
> >> >> But when I look at the structure and at the QM region
> coordinates,
> >> >> there
> >> >> seems to be enough space. There seems to be a conflict between
> the
> >> >> coordinate extremes written out in the first part of the output
> file
> >> >> (or
> >> >> the qmmm_region.pdb file), and the bounds written out in the
> latter
> >> >> part
> >> >> of the output file:
> >> >>
> >> >> ERROR: QM region + cutoff larger than box dimension:
> >> >> QM-MM Cutoff = 4.0000
> >> >> Coord Lower Upper Size Radius of largest sphere
> >> inside
> >> >> unit
> >> >> cell
> >> >> X -5.632 13.150 18.782 11.146
> >> >> Y -5.431 13.671 19.102 11.146
> >> >> Z -15.168 14.794 29.962 11.146
> >> >>
> >> >> To hone in on the problem, I set up a run that crashes on the
> second
> >> >> step.
> >> >> So
> >> >> 1) the initial qm region positions are written in the output file
> >> >> 2) the system takes one step, and writes "qmmm_region.pdb", the
> >> >> corresponding pdb file
> >> >> 3) the system crashes on the 2nd step, writing the bounds
> violation
> >> in
> >> >> the
> >> >> output file.
> >> >>
> >> >> Assuming positions barely change in one step, there seems to be a
> >> >> significant conflict within the code about where it thinks the
> >> bounds
> >> >> are?
> >> >>
> >> >> I attached the output files
> >> >>
> >> >> Thanks in advance for any help.
> >> >>
> >> >> Andrew Petersen
> >> >
> >> >
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >
> >>
> >>
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> >
>
>
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Received on Thu Apr 29 2010 - 06:30:03 PDT
