[gmx-users] position restraints

[Justin A. Lemkul]

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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