From: Xiaoqing Wang (namdwxq_at_126.com)
Date: Sun May 15 2005 - 07:01:13 CDT
Dear Sir/Madam,
We have recently started to use NAMD to run macromolecular simulations. NAMD is a powerful and user-friendly software, and we really like it.
I have one question regarding computing with NAMD on AMD64.
I have recently compiled Charm++/NAMD(with fftw-2.1.5 tcl8.3
plugins-LINUXAMD64) on AMD64. I test namd2 with input files which
downloaded from web site:
http://www.ks.uiuc.edu/Research/namd/tutorial/NCSA2002/hands-on/sample/
I submit the job using "qsub w"
w
----------------------------------------------------------------
#!/bin/bash
#PBS -N w
#PBS -o output
#PBS -e error
#PBS -q work
#PBS -l ncpus=2
#PBS -l nodes=1
#PBS -l walltime=10:00:00
cd /home/xqwang/work/example
/usr/local/mpich_pg/bin/mpirun -machinefile $PBS_NODEFILE -np 2
/home/xqwang/namd/NAMD_2.5_Source/Linux-amd64-MPI/namd2
equil.namd>equil.log
----------------------------------------------------------------
But "namd2" seems not to work well.
equil_out.xst
----------------------------------------------------------------
# NAMD extended system trajectory file
#$LABELS step a_x a_y a_z b_x b_y b_z c_x c_y c_z o_x o_y o_z
2000 30 0 0 15 25.98 0 0 0 64 0 0 0
2100 30 0 0 15 25.98 0 0 0 64 0 0 0
2200 30 0 0 15 25.98 0 0 0 64 0 0 0
2300 30 0 0 15 25.98 0 0 0 64 0 0 0
2400 30 0 0 15 25.98 0 0 0 64 0 0 0
2500 30 0 0 15 25.98 0 0 0 64 0 0 0
2600 30 0 0 15 25.98 0 0 0 64 0 0 0
2700 30 0 0 15 25.98 0 0 0 64 0 0 0
2800 30 0 0 15 25.98 0 0 0 64 0 0 0
2900 30 0 0 15 25.98 0 0 0 64 0 0 0
3000 30 0 0 15 25.98 0 0 0 64 0 0 0
3100 30 0 0 15 25.98 0 0 0 64 0 0 0
3200 30 0 0 15 25.98 0 0 0 64 0 0 0
3300 30 0 0 15 25.98 0 0 0 64 0 0 0
3400 30 0 0 15 25.98 0 0 0 64 0 0 0
3500 30 0 0 15 25.98 0 0 0 64 0 0 0
3600 30 0 0 15 25.98 0 0 0 64 0 0 0
3700 30 0 0 15 25.98 0 0 0 64 0 0 0
3800 30 0 0 15 25.98 0 0 0 64 0 0 0
3900 30 0 0 15 25.98 0 0 0 64 0 0 0
4000 30 0 0 15 25.98 0 0 0 64 0 0 0
4100 30 0 0 15 25.98 0 0 0 64 0 0 0
4200 30 0 0 15 25.98 0 0 0 64 0 0 0
4300 30 0 0 15 25.98 0 0 0 64 0 0 0
4400 30 0 0 15 25.98 0 0 0 64 0 0 0
4500 30 0 0 15 25.98 0 0 0 64 0 0 0
4600 30 0 0 15 25.98 0 0 0 64 0 0 0
4700 30 0 0 15 25.98 0 0 0 64 0 0 0
4800 30 0 0 15 25.98 0 0 0 64 0 0 0
4900 30 0 0 15 25.98 0 0 0 64 0 0 0
5000 30 0 0 15 25.98 0 0 0 64 0 0 0
5000 30 0 0 15 25.98 0 0 0 64 0 0 0 0 0 0 0 0 0
5100 33.0438 0 0 16.5219 28.616 0 0 0 61.8588 0 0 0 0.000729971
0.000729971 -0.000331682 0 0 0
5200 35.6344 0 0 17.8172 30.8594 0 0 0 59.7898 0 0 0 0.00085569
0.00085569 -0.000278095 0 0 0
5300 38.8734 0 0 19.4367 33.6644 0 0 0 57.8525 0 0 0 0.000847672
0.000847672 -0.000461775 0 0 0
5400 42.6974 0 0 21.3487 36.9759 0 0 0 55.4314 0 0 0 0.000863158
0.000863158 -0.000519883 0 0 0
5500 47.7802 0 0 23.8901 41.3777 0 0 0 53.0653 0 0 0 0.00102197
0.00102197 -0.000181384 0 0 0
5600 53.4207 0 0 26.7104 46.2623 0 0 0 50.5934 0 0 0 0.000992159
0.000992159 -0.000417692 0 0 0
5700 60.4608 0 0 30.2304 52.359 0 0 0 48.2803 0 0 0 0.00127705
0.00127705 -0.000551151 0 0 0
5800 67.9099 0 0 33.955 58.81 0 0 0 45.7991 0 0 0 0.00112851 0.00112851
-0.000681137 0 0 0
5900 75.9974 0 0 37.9987 65.8138 0 0 0 43.2843 0 0 0 0.000990431
0.000990431 -0.000696884 0 0 0
------------------------------------------------------------------------
error file
------------------------------------------------------------------------
/usr/local/mpich_pg/bin/mpirun: line 77: cannot create temp file for
here document: Permission denied
FATAL ERROR: Periodic cell has become too small for original patch grid!
Possible solutions are to restart from a recent checkpoint,
increase margin, or disable useFlexibleCell for liquid simulation.
[0] MPI Abort by user Aborting program !
[0] Aborting program!
FATAL ERROR: Periodic cell has become too small for original patch grid!
Possible solutions are to restart from a recent checkpoint,
increase margin, or disable useFlexibleCell for liquid simulation.
[1] MPI Abort by user Aborting program !
[1] Aborting program!
------------------------------------------------------------------------
And the attachment file "equil.log"
What's wrong with namd2?
Any tips would be greatly appreciated!
Sincerely,
Xiaoqing
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