NAMD is too slow?!

From: DimitryASuplatov (
Date: Sun Mar 29 2009 - 04:37:39 CDT


I am calculating a system of 700 aa protein in a water box (15
angstroms around the protein), using electrostatic switch 10A and
cutoff 15 A. PME is off. The estimation on 64 Intel Xeon 3Gz cores is
0.44 days/ns and about 4 days for 10ns. I was using intel compilers,
mvapich and the following options
CHARMM: ./build charm++ mpi-linux-ia64 icc ifort --no-shared -O
-DCMK_OPTIMIZE=1 -I/usr/lib/mvapich-intel-x86_64/include/
NAMD: ./config tcl fftw Linux-ia64-MPI-GM-icc
and I use mpirun -np 64 namd2 <config> to run the program

I was using gromacs previosly and I find it to be 10 times faster.

My question is -
is this a common estimate for a system of that size or I have problems
with my cluster or my installation?


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