Do you see any error messages - perhaps in the PBS log files for the job?
> On Feb 6, 2015, at 1:28 AM, Shreeramesh <shreeramesh.gmail.com> wrote:
>
> 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 - 13:00:02 PST
