[gmx-users] SHAKE and pbc=full
David van der Spoel
spoel at xray.bmc.uu.se
Thu Sep 8 13:38:01 CEST 2005
On Thu, 2005-09-08 at 04:01 -0700, leafyoung81-group at yahoo.com wrote:
> 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?
> Yang Ye
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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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