Hi Stacyann,
You can try "nmropt=1" flag and rerun your heating steps.
I see you are using ntt=1, which could be dangerous since you are using
implicit solvation (igb=1). I would advise, using ntt=3 (langevin dynamics)
with gamma_ln=2.0 or 3.0 (collision frequency).
See this, paraphasing from the Amber16 manual
ntt
= 1 Constant temperature, using the weak-coupling algorithm.[335] A single
scaling factor is used
for all atoms. Note that this algorithm just ensures that the total kinetic
energy is appropriate
for the desired temperature; it does nothing to ensure that the temperature
is even over all parts
of the molecule. Atomic collisions will tend to ensure an even temperature
distribution, but
this is not guaranteed, and there are many subtle problems that can arise
with weak temperature
coupling.[336] Using ntt=1 is especially dangerous for generalized Born
simulations, where
there are no collisions with solvent to aid in thermalization.) Other
temperature coupling options
(especially ntt=3) should be used instead.
Regards
*Elvis Martis* PhD Student, Bombay College of Pharmacy
[image: photo] Email: elvis_bcp.elvismartis.in <elvis_bcp.elvismartis.in>
Website: http://www.elvismartis.in <http://www.elvismartis.in/>
group website: http://www.profeccoutinho.net.in/
Address:
Kalina, Santa Cruz [E]
, Mumbai, 400 098, INDIA
Alt. e-mail: emartis12.live.com
<
https://in.linkedin.com/in/elvisadrianmartis>
On 3 November 2016 at 09:14, Stacyann Nelson <mitize2000.yahoo.com> wrote:
> Hi Elvis,
>
> T
>
> his 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
> [image: photo] Email: elvis_bcp.elvismartis.in <elvis_bcp.elvismartis.in>
> Website: http://www.elvismartis.in <http://www.elvismartis.in/>
> group website: http://www.profeccoutinho.net.in/
> Address:
>
> Kalina, Santa Cruz [E]
> , Mumbai, 400 098, INDIA
>
> Alt. e-mail: emartis12.live.com
> <https://in.linkedin.com/in/elvisadrianmartis>
>
>
> 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 - 21:30:02 PDT
