[gmx-users] problems with parallel mdrun
singh at biophysik.chemie.uni-dortmund.de
Wed Aug 8 20:28:25 CEST 2007
Dear gmx users,
I am using a current CVS version of Gromacs and using the newly introduced
options for simulations with walls. I am facing the following two
I get the following errors while using paralled version of mdrun compiled
mpirun -np 4 mdrun_d_mpi -np 4 -v -deffnm EQUI1
Program mdrun_d_mpi, VERSION 3.3.99_development_20070720
Source code file: gmx_parallel_3dfft.c, line: 90
nx (50) and ny (50) must be divisible by the number of nodes (4).
I am using a cubic box of 5nm and grid spacing is 0.1. The simulations
runs fine if i use 5 nodes
I am using a machines with 2 dual xeon processors so -np 4 is more
appropriate for my sytems.
Is there any way to use -np 4 without changing the gridspacing
or box size?
second question is regarding wall_denstiy option.
As i understood from the manual the wall density is a number density in
units of number/nm2 in case of 10-4 potential
and is number/nm3 in case of 9-3 potential.
please correct me if i am wrong.
Thank you in advance
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