From: ipsita basu (ibasu788_at_gmail.com)
Date: Thu May 06 2010 - 05:32:13 CDT
Thanks a lot for your reply. I tried timestep 1 before your reply and
the job was running fine without giving any error. But the structure
become distorted, it squeezes along z axis. Now according to your
reply I am fix the langevin temp to zero and heating the system
gradually by loop. This part is given below:
# gradual temp increase
run 1000
for { set TEMP 0 } { $TEMP <= 290 } {incr TEMP 1 } {
langevinTemp $TEMP
run 1000
I hope this will not disturb the structure.
Any suggestion from your end would be appreciated.
On 5/5/10, muniyamuthu.raviprasad_at_ndsu.edu
<muniyamuthu.raviprasad_at_ndsu.edu> wrote:
> Hi
>
> According to your configuration file, your langevinTemp (290) is too high.
> It applies large force in the system and it moves atom very fast.
>
> try these
>
> 1] Apply the temperature step by step (100 200 290 ..)
> 2] You can use smaller time step (1 fs or 0.5 fs)
> 3] make sure all atoms inside the cell basis vector
> 4] use Velocity control or Temperature control with Langivin Dynamics
>
> I hope it will work
>
> Ravi
>
>
>
> > Hi all,
> > I have been getting an error during the heating after 50000
> > steps of minimization. The error is like this :
> >
> > ENERGY: 50080 6900.3852 6903.3658 3540.2068
> > 50.1815 -133358.2452 13139.9822 18.9646 0.0000
> > 12009.7203 -90795.4389 104.3929 -89735.2082
> > -89012.8941 102.7365 3460.7576 1431.2232
> > 516713.1384 1440.3727 1949.4518
> >
> > ERROR: Atom 568 velocity is 24014.9 41973.4 26943.1 (limit is 5000)
> ERROR: Atom 574 velocity is -23402.1 -44094 -37182.6 (limit is 5000)
> ERROR: Atom 576 velocity is -461.405 -5353.41 1739.84 (limit is 5000)
> ERROR: Atoms moving too fast; simulation has become unstable.
> > ERROR: Exiting prematurely.
> >
> > I have peptide-bilayer system, and I check the pbc condition which is
> allright.
> > I would like to know if anyone knows how to solve this problem as I
> > really need it. I am attaching herewith the input file.
> >
> > --
> > Ipsita Basu
> > Research Fellow
> > c/o : Dr. Chaitali Mukhopadhyay
> > Rajabazar Science College
> > 92 APC Road
> > Kolkata - 700009
> >
>
>
>
>
>
-- Ipsita Basu Research Fellow c/o : Dr. Chaitali Mukhopadhyay Rajabazar Science College 92 APC Road Kolkata - 700009
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