Dear Amber-users,
I've done energy minimization of my system (~70,000 atoms, including water), and
then run MD with restraints on the solute by using sander. And then, I was
trying to simulate this system, testing with pmemd and sander with parallel and
no parallel. Sander and pmemd passed example test, so there may be no problem
with installation. When I ran the simulation with sander at single CPU, it
nicely worked. But, in ohter cases, I got two problems.
1) When I ran sander in one CPU, it nicely worked. However, when I ran sander in
multiple CPUs, I saw CPUs run but coulnd't see any output files (.out and
..mdcrd). I'm sure that I made right directory for output files. Could you tell
me why I can't see the output files in the directory
(/home/leehk/run/g5ace90-par4)? This is script file.
---------------------------
#PBS -S /bin/bash
#PBS -l nodes=2,walltime=500:00:00
#PBS -q protein
#PBS -N sand-cpu4
#PBS -j oe
#PBS -M leehk.umich.edu
#PBS -m abe
#
echo "I ran on `hostname`"
cat $PBS_NODEFILE
#
export GMPICONF=/home/leehk/.gmpi/$PBS_JOBID
export PATH=/usr/cac/mpich.eth/bin:$PATH
#
cd /home/leehk/run/g5ace90-par4
mpirun -np 4 -machinefile $PBS_NODEFILE /home/leehk/exe.eth/sander -O -i md2.in
-o md2.out -p g5ace90.prmtop -c md1.rst -r g5ace90-md0.rst -x g5ace90-md0.mdcrd
#
---------------------------
2) When I ran pmemd at one CPU or multiple CPUs, I saw CPUs run, but when I
checked .out file, I saw that .out file stopped like below. Since this system
work with sander, I cannot understand why it didn't work with pmemd.
I also attach my script file.
-----------------------------
-------------------------------------------------------
Amber 8 SANDER Scripps/UCSF 2004
-------------------------------------------------------
| PMEMD implementation of SANDER, Release 8.0
| Run on 04/26/2005 at 15:28:30
[-O]verwriting output
File Assignments:
| MDIN: md2.in
| MDOUT: md2.out
| INPCRD: md1.rst
| PARM: g5ace90.prmtop
| RESTRT: g5ace90-md0.rst
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: g5ace90-md0.mdcrd
| MDINFO: mdinfo
Here is the input file:
dendrimer : 2ns of MD
&cntrl
imin = 0, irest = 0, ntx = 7,
ntb = 2, pres0 = 1.0, ntp = 1,
taup = 5.0,
cut = 10, ntr = 0,
ntc = 2, ntf = 2,
tempi = 298.0, temp0 = 298.0,
ntt = 3, gamma_ln = 1.0,
nstlim = 1000000, dt = 0.002,
ntpr = 500, ntwx = 500, ntwr = 20000
/
| Largest sphere to fit in unit cell has radius = 40.001
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
getting new box info from bottom of inpcrd
NATOM = 63187 NTYPES = 11 NBONH = 60807 MBONA = 2367
NTHETH = 6554 MTHETA = 2860 NPHIH = 10308 MPHIA = 3601
NHPARM = 0 NPARM = 0 NNB = 105162 NRES = 19366
NBONA = 2367 NTHETA = 2860 NPHIA = 3601 NUMBND = 15
NUMANG = 26 NPTRA = 7 NATYP = 14 NPHB = 1
IFBOX = 2 NMXRS = 635 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Coordinate Index Table dimensions: 17 17 17
| Direct force subcell size = 5.7636 5.7636 5.7636
BOX TYPE: TRUNCATED OCTAHEDRON
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
DEU
General flags:
imin = 0, nmropt = 0
Nature and format of input:
ntx = 7, irest = 0, ntrx = 1
Nature and format of output:
ntxo = 1, ntpr = 500, ntrx = 1, ntwr = 20000
iwrap = 0, ntwx = 500, ntwv = 0, ntwe = 0
ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0
Potential function:
ntf = 2, ntb = 2, igb = 0, nsnb = 25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 10.00000, intdiel = 1.00000
scnb = 2.00000, scee = 1.20000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
------------------------------------
Script file is below.
-------------------------------------
#PBS -S /bin/bash
#PBS -l nodes=1,walltime=500:00:00
#PBS -q protein
#PBS -N sanpme1cpu
#PBS -j oe
#PBS -M leehk.umich.edu
#PBS -m ae
echo "I ran on `hostname`"
cd /home/leehk/run/g5ace90-pme
/home/leehk/exe.ser/pmemd -O -i md2.in -o md2.out -p g5ace90.prmtop -c md1.rst
-r g5ace90-md0.rst -x g5ace90-md0.mdcrd &
wait
-------------------------------------
best,
Hwankyu.
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Received on Tue Apr 26 2005 - 21:53:00 PDT
