[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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> >
> >
> >
> > ========================================
> >
> > 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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