Hi Elvis,
This is my input file
Stage1 heating to 50 K &cntrl imin=0,irest=0, ntx=1, nstlim=50000, dt= .002, ntc=2, ntf=2, ntt=1, tautp=1.0, tempi=200.0, temp0=250.0, ntpr=50, ntwx=50, ntb=0, igb=1, cut=999.0, /~~
This is my batch submit script:
#!/bin/bash#SBATCH --partition=compute#SBATCH --nodes=4#SBATCH --tasks-per-node=1#SBATCH -t 48:00:00#SBATCH -o RADA.out #SBATCH -e RADA.err#SBATCH --export=ALLmodule unload intelmodule load amberAMBERHOME=/home/jpg/opt/comet/amberibrun sander.MPI -O -i RA48_Heat_5.in -c heat_4_RA48.rst -p RA48_noH.top -o heat_5_RA48.out -r heat_5_RA48.rst
~
Regards
Stacyann
On Wednesday, November 2, 2016 11:08 PM, Elvis Martis <elvis_bcp.elvismartis.in> wrote:
Hi,
Can you post your input file (heating protocol) as well?
It would be easier to point out what could have possibly gone wrong.
Regards
*Elvis Martis* PhD Student, Bombay College of Pharmacy
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On 3 November 2016 at 06:02, Stacyann Nelson <mitize2000.yahoo.com> wrote:
> Hi All,
> I am interested in running MD simulations on two strands of a small
> amyloid peptide. I am heating up the system from 50 -310K.However I am
> getting error while heating up the system at 200 -250.
>
> 3. ATOMIC COORDINATES AND VELOCITIESERROR: Problem reading coordinates or
> velocities from heat_4_RA48.rst
> I have restarted the process 3 times but getting the same error.
> Can I have some assistance, please?
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>
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Received on Wed Nov 02 2016 - 21:00:02 PDT
