Re: [AMBER] Error in the production of heat.rst file

From: Stacyann Nelson <>
Date: Thu, 3 Nov 2016 03:44:47 +0000 (UTC)

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 -c heat_4_RA48.rst -p -o heat_5_RA48.out -r heat_5_RA48.rst

    On Wednesday, November 2, 2016 11:08 PM, Elvis Martis <> wrote:

Can you post your input file (heating protocol) as well?
It would be easier to point out what could have possibly gone wrong.


*Elvis Martis*  PhD Student, Bombay College of Pharmacy
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 Kalina, Santa Cruz [E]
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On 3 November 2016 at 06:02, Stacyann Nelson <> 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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Received on Wed Nov 02 2016 - 21:00:02 PDT
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