[gmx-users] SHAKE and pbc=full

[David van der Spoel]

On Thu, 2005-09-08 at 05:43 -0700, leafyoung81-group at yahoo.com wrote:
> --- David van der Spoel <spoel at xray.bmc.uu.se>
> wrote:
> 
> > On Thu, 2005-09-08 at 04:01 -0700,
> > leafyoung81-group at yahoo.com wrote:
> > > Hi,
> > > 
> > > In my system, I constructed a rigid structure
> > (quite
> > > big, 110x110x50 A), any two of the atoms are
> > bonded
> > > and are converted to constraints using
> > > constraints=all-bonds. I used SHAKE because
> LINCS
> > > could not do so.
> > > 
> > > When doing MD with pbc=xyz, when part of the
> > structure
> > > moving outside the boundary, the atoms exploded.
> > When
> > > I switched to pbc=full, grompp gives me "can not
> > do
> > > full pbc with Shake, use Lincs".
> > > 
> > > Is there any work-around for this issue?
> > why does it not work with lincs?
> I have eight atoms and defined 28 constraints. LINCS
> could not stablize them. It gives information like
> 
>  atom 1 atom 2  angle  previous, current, constraint
> length
>    2249   2250  179.9    4.3182 387.7610     11.0000
>    2249   2251  179.8    3.0487 245.6509      7.7780
>    2249   2252  179.9    3.0463 245.5878      7.7780
>    2249   2253  165.5    1.6592 103.3634      4.2240
>    2249   2254  174.0    4.1575 355.4330     10.5750
> 
> I tried adjusting lincs_order and lincs_iter.
> Increasing either of them will just make it worse.
> 
Increase the number of exclusions.

(and by the way please keep this discussion on the list)

> But SHAKE is just fine for my system.
> 
> Yang Ye
> 
> > > 
> > > Thanks.
> > > 
> > > Yang Ye
> > > 
> > > 
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> > -- 
> > David.
> >
> ________________________________________________________________________
> > David van der Spoel, PhD, Assoc. Prof., Molecular
> > Biophysics group,
> > Dept. of Cell and Molecular Biology, Uppsala
> > University.
> > Husargatan 3, Box 596,          75124 Uppsala,
> > Sweden
> > phone:  46 18 471 4205          fax: 46 18 511 755
> > spoel at xray.bmc.uu.se    spoel at gromacs.org  
> > http://xray.bmc.uu.se/~spoel
> >
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> > 
> > 
> > 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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