[gmx-users] SHAKE and pbc=full

[leafyoung81-group at yahoo.com]

--- 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.

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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> 
> 
>