I started from the original pdb file without any wrapping. I changed the
mdp for the wall settings to:
pbc = xy
nwall = 2
wall-type = 9-3
wall-density= 5 5
wall-atomtype = OT OT
wall-r-linpot = 0.1
I notice that they are the hydrogen atoms of the same water molecule and
they may have been split by the PBC in the previous step. I'll prepare
the gro again. Thanks for your help.
Cheers
On 07/02/16 22:23, Justin Lemkul wrote:
On 7/2/16 4:20 PM, Stephen Chan wrote:
Hi Justin,
Just above
On 7/2/16 4:20 PM, Stephen Chan wrote:
Hi Justin,
Just above the fatal error message, there is some additional information:
Initializing Domain Decomposition on 112 ranks
Dynamic load balancing: auto
Will sort the charge groups at every domain (re)decomposition
Initial maximum inter
Hi Justin,
Just above the fatal error message, there is some additional information:
Initializing Domain Decomposition on 112 ranks
Dynamic load balancing: auto
Will sort the charge groups at every domain (re)decomposition
Initial maximum inter charge-group distances:
two-body bonded
On 7/2/16 3:50 PM, Stephen Chan wrote:
Dear all,
I'm running a simulation of a bilayer system and I would like to apply wall
condition to both xy planes (i.e. nwall = 2). On top of the normal MD settings,
I added a couple of lines to the mdp file:
pbc = xy
nwall = 2
Dear all,
I'm running a simulation of a bilayer system and I would like to apply
wall condition to both xy planes (i.e. nwall = 2). On top of the normal
MD settings, I added a couple of lines to the mdp file:
pbc = xy
nwall = 2
wall-type = 10-4
wall-density= 5
