Darrell Koskinen wrote:
Dear GROMACS-ians,
I have created an infinite graphene sheet and upon running grompp, I get
the following response:
/Warning: 1-4 interaction between 10085 and 10445 at distance 19.679
which is larger than the 1-4 table size 1.000 nm
Warning: 1-4 interaction between 9244 and 9963 at distance 19.553 which
is larger than the 1-4 table size 1.000 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
These are ignored for the rest of the simulation/
I assume that atoms from opposite ends of the simulation box are being
seen by GROMACS as being 1-4 neighbors as a result of the PBC, but the
shortest distance between the atoms is not being observed. Is this the
problem? Is this problem resulting in the system exploding? And, how do
I resolve this problem?
Did you use periodic_molecules = yes in your .mdp file?
Mark
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
