Re: [AMBER] How to use Amber in HPC

From: Elvis Martis <>
Date: Fri, 12 May 2017 11:40:31 +0000

You will need a pbs or torque script to submit any kind of jobs on the HPC.
The best would be to consult the system admin for the HPC
A typical pbs script will look like this, you must edit it to suit your system and your needs

#PBS -l nodes=2, ppn=2
#PBS -l walltime=50:00:00
#PBS -j oe
#PBS -q normal
#PBS -l pmem=2048MB
#PBS -l vmem=2048MB
set mpich_run = "XYZ/ mpirun" >>> consult system admin
set sander.MPI (pmemd.MPI) = "$AMBERHOME/bin/sander.MPI(or pmemd.MPI)" >> pointer for sander(or pmemd)
$mpich_run -machinefile $PBS_NODEFILE -np `wc -l < $PBS_NODEFILE`
$mpich_run -np $NSLOTS $sander.MPI (or $pmemd.MPI) -O -i INFILE -c INPUT_CORDINATE -o outfile -r output_coordinate -x trajectory_file >>> sander command will remain same

    Best Regards

Elvis Martis
Ph.D. Student (Computational Chemistry)
 at Bombay College of Pharmacy

A  Kalina, Santacruz [E], Mumbai 400098, INDIA
Skype. adrian_elvis12

-----Original Message-----
From: Garima Singh []
Sent: Friday, May 12, 2017 4:24 PM
Subject: [AMBER] How to use Amber in HPC

Dear Amber users,

I am using AMBER 14 in my system having processor* Intel® Xeon(R) CPU
E5-1607 v3 @ 3.10GHz* *× 4* . It takes a lot time to calculating the output.I want to run my Amber MD calculation in HPC. How to perform MD calculation using AMBER 14 in HPC .Which script file i need?

 Kindly provide your valuable suggestion

Garima Singh
AcSIR-PhD Fellow
Central Institute Of Medicinal And Aromatic Plant CSIR-CIMAP Lucknow

*INDIA* Please don't print this e-mail unless you really need to. Be Green !
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Received on Fri May 12 2017 - 05:00:02 PDT
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