Re: [gmx-users] Simulation Break => Due to bad domain decomposition ? (MPI) => Gromacs Version 3.3.3

2010-01-01 Thread Tsjerk Wassenaar
Hi Lin, > I used Gromacs version 3.3.3. There is no domain decomposition in gromacs 3.3.3. Furthermore, you again give no account of what you're doing in terms of command lines and don't show the grompp output. This is pointless. Tsjerk > My simulation system = one protein + 20 ligand + water

Re: [gmx-users] Simulation Break => Due to bad domain decomposition ? (MPI) => Gromacs Version 3.3.3

2010-01-01 Thread Mark Abraham
Chih-Ying Lin wrote: Hi I used Gromacs version 3.3.3. OK, but unless you need scientific continuity with earlier work, use the much faster 4.0.7. Additionally, domain decomposition was not implemented before 4.0, so either you're mistaken about your subject line, or you're using a 4.0.x

[gmx-users] Simulation Break => Due to bad domain decomposition ? (MPI) => Gromacs Version 3.3.3

2010-01-01 Thread Chih-Ying Lin
Hi I used Gromacs version 3.3.3. My simulation system = one protein + 20 ligand + water molecules ( 7x 7x 7 ) MPI setting => #PBS -l nodes=4:ppn=4,arch=x86_64 => 16 nodes in total After doing the energy minimization, => the potential energy is extremely high ( say, ten to the 9th order ) I visual