[gmx-users] position restraints
Justin A. Lemkul
jalemkul at vt.edu
Thu Apr 24 14:19:24 CEST 2008
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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========================================
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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