[gmx-users] Not all bonded interactions have been properly assigned to the domain decomposition cells

Hi ALL, I have made a CGMD system with multiple copies of a single protein in bilayer, by replicating the monomer using genconf in the X-Y plane. After running CGMD for about 100 ns, I am getting the following error:

Re: [gmx-users] Not all bonded interactions have been properly assigned to the domain decomposition cells

Although a bit worrying the curvature of your bilayer is not responsible for the error message you are seeing. to solve the problem you have to increase to use the -rrd option (see manual for explanation). Typicaly a value of 1.4 to 1.6 should be fine. On Aug 16, 2010, at 12:16 PM, Anirban

Re: [gmx-users] Not all bonded interactions have been properly assigned to the domain decomposition cells

Thanks a lot XAvier for clarifying my doubt. You mean to say -rdd option with mdrun, right? And why does this curvature of the membrane occurs? Thanks a lot once again. Regards, Anirban On Mon, Aug 16, 2010 at 3:53 PM, XAvier Periole x.peri...@rug.nl wrote: Although a bit worrying the

Re: [gmx-users] Not all bonded interactions have been properly assigned to the domain decomposition cells

Anirban Ghosh wrote: Hi ALL, I have made a CGMD system with multiple copies of a single protein in bilayer, by replicating the monomer using genconf in the X-Y plane. After running CGMD for about 100 ns, I am getting the following error:

Re: [gmx-users] Not all bonded interactions have been properly assigned to the domain decomposition cells

On Aug 16, 2010, at 1:33 PM, Anirban Ghosh wrote: Thanks a lot XAvier for clarifying my doubt. You mean to say -rdd option with mdrun, right? yes And why does this curvature of the membrane occurs? No idea! Thanks a lot once again. Regards, Anirban On Mon, Aug 16, 2010 at 3:53 PM,

[gmx-users] Not all bonded interactions have been properly assigned to the domain decomposition cells

Hi , I am getting the following error when I try to run in parallel (I've tried with 8 and 2 nodes and get the same). Not all bonded interactions have been properly assigned to the domain decomposition cells But my simulation works when I run in serial. I'm using gromacs 4.0.5. I am

Re: [gmx-users] Not all bonded interactions have been properly assigned to the domain decomposition cells

Jennifer Williams wrote: Hi , I am getting the following error when I try to run in parallel (I've tried with 8 and 2 nodes and get the same). Not all bonded interactions have been properly assigned to the domain decomposition cells But my simulation works when I run in serial. I'm using