Gurpreet Singh wrote:
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
problems.
You should send separate emails for each problem, with different subject
headings, so that people with relevant expertise have the maximum chance
of seeing your problem. The second problem here has nothing to do with
your email subject line...
I get the following errors while using paralled version of mdrun compiled
with openmpi.
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
Fatal error:
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?
No. I'm guessing your .mdp file is trying to specify nx/ny/nz, rather
than the grid spacing. If you specify the latter, grompp will take care
of this issue so that you get the largest allowable spacing smaller than
(or equal to) the requested grid spacing.
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.
I don't know.
Mark
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