Robert Johnson wrote:
Hello everyone,
I'm performing a simulation that includes a 2D infinite SiO2
substrate. I'm not interested in the high frequency motion of the
substrate bonds, so I'm applying position restraints to all the SiO2
atoms. I have other molecules in the system such as water and DNA that
require hydrogen bond restraints. However, I'm getting the following
error when trying to run the system across several nodes:
Fatal error:
Shake block crossing node boundaries
constraint between atoms (1680,1716)
The atoms listed are in the substrate. Since I'm already restraining
the substrate atoms, I don't really need to constrain the Hbonds in
the SiO2. Is there any way to apply Hbond restraints only to a group
of atoms?
Alternatively, how does Gromacs decide which bonds contain hydrogen? I
could just alter the topology file for the substrate to trick Gromacs
into thinking that the hydrogens in the SiO2 are really a different
type of atom.
Thanks,
Bob Johnson
_______________________________________________
gmx-users mailing list [email protected]
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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Bob,
try using
constraints = all-bonds,
or make sure that your charge groups overlap with the constraint groups.
--
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
_______________________________________________
gmx-users mailing list [email protected]
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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
