[gmx-users] SHAKE and pbc=full

[David van der Spoel]

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?
> 
> 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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++