[gmx-users] position restraints
Justin A. Lemkul
jalemkul at vt.edu
Thu Apr 24 14:30:48 CEST 2008
Quoting chandrabhan seniya <chandrabhanseniya at gmail.com>:
> what is yr real prob tell me?
No need to get confrontational; my reply was not intended to be insulting. Mark
and I have been putting forth some effort to help our friend Gadi here by
extracting some detail that may be useful to document in the list archives.
Posting advice to ignore the problem, that everything will be fine, etc, may
result in someone searching for help, finding your post about ignoring the
problem, and trying to proceed. My response was simply that errors that cause
simulations to crash typically shouldn't be ignored with the belief that they
will resolve themselves. Just my $0.02, and everyone hereafter is free to take
it or leave it.
-Justin
>
>
> On Thu, Apr 24, 2008 at 5:49 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
> > Quoting chandrabhan seniya <chandrabhanseniya at gmail.com>:
> >
> > > no prob you wait for some time it will write topology file and the
> > proceed
> > > further..
> >
> > I think that a lipid molecule trying to tear itself apart at step 0 would
> > fall
> > under the category of a "problem," and it will not disappear on it's own
> > if we
> > conveniently ignore it...
> >
> > >
> > > On Thu, Apr 24, 2008 at 5:04 PM, <gadies at fh.huji.ac.il> wrote:
> > >
> > > > Hi,
> > > >
> > > > The full mdrun output when the simulation blows up is:
> > > >
> > > > Step 0, time 0 (ps) LINCS WARNING
> > > > relative constraint deviation after LINCS:
> > > > max inf (between atoms 6 and 7) rms inf
> > > > bonds that rotated more than 30 degrees:
> > > > .
> > > > .
> > > > .
> > > > Warning: 1-4 interaction between 1 and 6 at distance
> > > > 324490777485109120.000 which is larger than the 1-4 table size 1.000
> > nm
> > > > These are ignored for the rest of the simulation
> > > > This usually means your system is exploding,
> > > > if not, you should increase table-extension in your mdp file
> > > >
> > > > Thanks Gadi
> > > >
> > > > Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:
> > > >
> > > >
> > > > > Did your minimization converge to a nice, negative potential energy?
> > > > > Also, what
> > > > > is the full mdrun output when the simulation blows up? You've
> > quoted
> > > > > the last
> > > > > bit, but it would be more informative to see the whole output, or at
> > > > > least a
> > > > > description of it (i.e., LINCS warnings).
> > > > >
> > > > > -Justin
> > > > >
> > > > > Quoting gadies at fh.huji.ac.il:
> > > > >
> > > > >
> > > > > > Hi,
> > > > > >
> > > > > > I tried using no temperature coupling and no constraints, that did
> > not
> > > > > > help.
> > > > > > If I run the simulation without the position restraints it works
> > OK.
> > > > > > Could there by something wrong with the posre file (I'll attach it
> > at
> > > > > > the end of the email).
> > > > > > I want one of the atoms in the lipid to stay in one place and the
> > rest
> > > > > > to wiggle around it. Is there any other way to do that which is
> > not
> > > > > > position restraints.
> > > > > >
> > > > > > Thanks Gadi
> > > > > >
> > > > > >
> > > > > > [ position_restraints ]
> > > > > > ; atom type fx fy fz
> > > > > > 1 1 0 0 0
> > > > > > 2 1 0 0 0
> > > > > > 3 1 0 0 0
> > > > > > 4 1 0 0 0
> > > > > > 5 1 0 0 0
> > > > > > 6 1 0 0 0
> > > > > > 7 1 0 0 0
> > > > > > 8 1 1000.0 1000.0 1000.0
> > > > > > 9 1 0 0 0
> > > > > > 10 1 0 0 0
> > > > > > 11 1 0 0 0
> > > > > > 12 1 0 0 0
> > > > > > 13 1 0 0 0
> > > > > > 14 1 0 0 0
> > > > > > 15 1 0 0 0
> > > > > > 16 1 0 0 0
> > > > > > 17 1 0 0 0
> > > > > > 18 1 0 0 0
> > > > > > 19 1 0 0 0
> > > > > > 20 1 0 0 0
> > > > > > 21 1 0 0 0
> > > > > > 22 1 0 0 0
> > > > > > 23 1 0 0 0
> > > > > > 24 1 0 0 0
> > > > > > 25 1 0 0 0
> > > > > > 26 1 0 0 0
> > > > > > 27 1 0 0 0
> > > > > > 28 1 0 0 0
> > > > > > 29 1 0 0 0
> > > > > > 30 1 0 0 0
> > > > > > 31 1 0 0 0
> > > > > > 32 1 0 0 0
> > > > > > 33 1 0 0 0
> > > > > > 34 1 0 0 0
> > > > > > 35 1 0 0 0
> > > > > > 36 1 0 0 0
> > > > > > 37 1 0 0 0
> > > > > > 38 1 0 0 0
> > > > > > 39 1 0 0 0
> > > > > > 40 1 0 0 0
> > > > > > 41 1 0 0 0
> > > > > > 42 1 0 0 0
> > > > > > 43 1 0 0 0
> > > > > > 44 1 0 0 0
> > > > > > 45 1 0 0 0
> > > > > > 46 1 0 0 0
> > > > > > 47 1 0 0 0
> > > > > > 48 1 0 0 0
> > > > > > 49 1 0 0 0
> > > > > > 50 1 0 0 0
> > > > > >
> > > > > > Quoting Mark Abraham <Mark.Abraham at anu.edu.au>:
> > > > > >
> > > > > > > gadies at fh.huji.ac.il wrote:
> > > > > > >
> > > > > > > Please generate replies to the mailing list sensibly. It's very
> > hard
> > > > > > to
> > > > > > > work out who you are quoting where in this email. It'd be easy
> > just
> > > > > > to
> > > > > > > ignore it, and that's the last thing you should want.
> > > > > > >
> > > > > > >> Hello,
> > > > > > >>
> > > > > > >> I'm trying to run a simulation with one lipid molecule in a
> > fixed
> > > > > > >> simulation box without pbc.
> > > > > > >> I set position restraints on one of the atoms and I seem to
> > keep on
> > > > > > >> getting the following error:
> > > > > > >
> > > > > > > Why do you want MD of a single lipid and a position restraint on
> > one
> > > > > > > atom? If you just want to see a lipid wiggle around, then don't
> > > > > > create
> > > > > > > more numerical complexity.
> > > > > > >
> > > > > > >> The lipid is DPPC.The .itp file I got from a coworker that used
> > it
> > > > > > >> before for membrane MD simulations.
> > > > > > >> To minimize the system I used steepest descent with the
> > following
> > > > > > >> parameters:
> > > > > > >
> > > > > > > Well if your grompp and mdrun completed successfully and without
> > > > > > > warnings then you've probably got an OK topology and structure.
> > > > > > >
> > > > > > > The combination of all bond constraints, a single lipid in
> > vacuo,
> > > > > > > temperature coupling and a single position restraint sounds like
> > a
> > > > > > > recipe for a numerical disaster, i.e. blowing up. Try with fewer
> > of
> > > > > > > those things applied, or get a more physically-reasonable
> > system,
> > > > > > like
> > > > > > > a whole membrane.
> > > > > > >
> > > > > > > Mark
> > > > > > > _______________________________________________
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> > > > > >
> > > > >
> > > > >
> > > > > ========================================
> > > > >
> > > > > Justin A. Lemkul
> > > > > Graduate Research Assistant
> > > > > Department of Biochemistry
> > > > > Virginia Tech
> > > > > Blacksburg, VA
> > > > > jalemkul at vt.edu | (540) 231-9080
> > > > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
> > > > >
> > > > > ========================================
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> > >
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> >
> >
> > ========================================
> >
> > Justin A. Lemkul
> > Graduate Research Assistant
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul at vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
> >
> > ========================================
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>
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
========================================
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