[gmx-users] position restraints
Justin A. Lemkul
jalemkul at vt.edu
Thu Apr 24 14:56:16 CEST 2008
Quoting gadies at fh.huji.ac.il:
> Hi,
>
> I minimized without restraints, could that be the problem?
> After the minimization I got a Potential Energy = -6.1434351e+02.
That seems fine. Basically, your lipid's headgroup is shearing itself apart
(which you can tell from the LINCS warnings). At this point, I could only
guess as to what's going wrong, which probably won't do you much good.
If you'd like to send me your structure, topologies, and .mdp file off-list, I'd
be happy to have a look at them.
-Justin
>
> Gadi
>
>
> Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:
>
> > 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
> >> >> > _______________________________________________
> >> >> > gmx-users mailing list gmx-users at gromacs.org
> >> >> > http://www.gromacs.org/mailman/listinfo/gmx-users
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> >> posting!
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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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>
>
>
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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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