Dear Sir,
I want to simulate the ligand (Anionic carboxylic acid) in AMBER.
When I proceed for MD upto 250000 steps, the job was stopped at 12000 steps
in md.out file
Please kindly help me to solve the above mentioned error
The script for minimization as follows
&cntrl
imin=1,
ntx=1,
irest=0,
maxcyc=2000,
ncyc= 1000,
ntpr=100,
ntwx=0,
cut= 12.0,
/
END
The script for Heating and equilibrium step​ as follows
&cntrl
imin= 0,
irest=0,
NTX=1,
ntb= 1,
ntp=0,
NTPR=500,
NTWX=500,
Tempi=0.0,
Temp0=300.0,
NTT=3,
gamma_ln=2.0,
NTC=2,
NTF=2,
cut= 12.0,
nmropt=1,
ig=-1,
nstlim=10000,
dt=0.002,
/
&wt type='TEMP0', istep1=0, istep2=9000, value1=0.0, value2=300.0 /
&wt type='TEMP0', istep1=9001, istep2=10000, value1=300.0, value2=300.0 /
&wt type='END' /
~
The script for md step as follows
&cntrl
imin=0,
irest=1,
NTX=5,
ntb=2,
ntp=1,
PRES0=1.0,
TAUP=2.0,
NTPR=500,
NTWX=500,
NTWR=500,
Tempi=300.0,
Temp0=300.0,
NTT=3,
gamma_ln=2.0,
ig=-1,
NTC=2,
NTF=2,
cut=12.0,
nstlim=2500000,
dt=0.002
/
The script for job submission as follows
#!/bin/bash
#PBS -N Lig
#PBS -q gpu
#PBS -l nodes=1:ppn=1:gpus=1:exclusive_process
#PBS -l walltime=72:00:00
#PBS -V
#PBS -k oe
echo $CUDA_VISIBLE_DEVICES
export CUDA_VISIBLE_DEVICES=`cat $PBS_GPUFILE | awk -F"-gpu" '{ printf
A$2;A=","}'`
#REMEMBER TO CHANGE ME FOR WHATEVER DIRECTORY YOU ARE RUNNING IN
cd /cbio/jclab/projects/collab/suri/ramesh/dend15-4
#AMBER
export AMBERHOME=/cbio/jclab/projects/collab/amber14
#Run the minimization with just CPU AMBER.
$AMBERHOME/bin/pmemd -O -i Mini.in -o Mini.out -p LIG_solvated.top -c
LIG_solvated.crd -r Mini.rst -inf Min.mdinfo
#Run MD using GPU AMBER.
$AMBERHOME/bin/pmemd.cuda -O -i Heating.in -o Heating.out -p
LIG_solvated.top -c Mini.rst -r Heating.rst -x Heating.mdcrd -inf
Heating.mdifo
$AMBERHOME/bin/pmemd.cuda -O -i md.in -o md.out -p LIG_solvated.top -c
Heating.rst -r md.rst -x md.mdcrd -infmd.info
Thanks & regards
*Dr. Ramesh M*
Email: shreeramesh.gmail.com
Mobile: 91 + (0) 9646469938 27+ (0) 844556164
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Received on Fri Feb 06 2015 - 01:30:05 PST
