[gmx-users] position restraints

chandrabhan seniya chandrabhanseniya at gmail.com
Thu Apr 24 13:41:58 CEST 2008 

no prob you wait for some time it will write topology file and the proceed
further..

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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> > >
> > >
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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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