Re: error : atom moving too fast

From: muniyamuthu.raviprasad_at_ndsu.edu
Date: Thu May 06 2010 - 09:35:02 CDT

It looks fine

Just a suggestion -----you may use [incr TEMP] fairly large value [50K]

Ravi

> 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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