[gmx-users] position restraints
Justin A. Lemkul
jalemkul at vt.edu
Thu Apr 24 13:38:19 CEST 2008
Quoting gadies at fh.huji.ac.il:
> 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
Basic information about this type of error can be found here (as well as several
hundred posts in the list archive):
http://wiki.gromacs.org/index.php/Errors#LINCS_warnings
How did you do your minimization, with or without restraints? Did it converge
to an acceptable potential energy?
-Justin
>
> 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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> >>
> >>
> >>
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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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>
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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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