[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 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)
Exclusion is considered and put into the energy_excl
group.
> 
> > But SHAKE is just fine for my system.
> > 
> > Yang Ye
> > 
> > > > 
> > > > Thanks.
> > > > 
> > > > Yang Ye
> > > > 
> > > > 
> > > >
> _______________________________________________
> > > > gmx-users mailing list
> > > > gmx-users at gromacs.org
> > > >
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > > Please don't post (un)subscribe requests to
> the
> > > list. Use the 
> > > > www interface or send it to
> > > gmx-users-request at gromacs.org.
> > > -- 
> > > 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
> > >
> >
>
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > > 
> > > 
> > > 
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the
> list. Use the 
> > www interface or send it to
> gmx-users-request at gromacs.org.
> -- 
> 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
>
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> 
> 
>