[gmx-users] position restraints

chandrabhan seniya chandrabhanseniya at gmail.com
Thu Apr 24 14:22:09 CEST 2008 

what is yr real prob tell me?


On Thu, Apr 24, 2008 at 5:49 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

> 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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