Re: error : atom moving too fast

From: muniyamuthu.raviprasad_at_ndsu.edu
Date: Fri May 14 2010 - 14:20:42 CDT

Hi

I would suggest this:

1] First increase the temperature in three steps
    - 0 to 100 K
    - 100 K to 200 K
    - 200 K to 290 K

2] while keeping the temperature at 290 increase the pressure in four steps
    - 0 to 0.25
    - 0.25 to 0.50
    - 0.5 to 0.75
    - 0.75 to 1.01325

I think this would help to understand the process easily. your idea is to
mimic your molecular model to real situation. It would be better if you
increase temperature and pressure step by step.

Important :
1] Every time when you increase the temperature or pressure you have to
use new coordinates and velocities. EX: take your minimized model and
increase the temperature to 100, finally you will get new coordinates new
velocities. use these files for your second increment 200 K and so on

2] when you increase pressure LangivinTemp and LangivinPistonTemp should
be equal.

If you have any difficulties to understand above writings, write to me
and send me your configuration file

Try this
Ravi

> Hi all,
> Thanks a lot for your reply. Now my job is running well and
> the structure is allright. But as I am just in the learning stage,so
> I want to be sure that's wheather I am doing the right job before
> running a simulation finally. After minimization I want to heat my
> system from 0 to 290K. My constant temp and pressure part is:
> langevin on ;# do langevin dynamics
> langevinDamping 10 ;# damping coefficient (gamma) of 5/ps
> langevinHydrogen no ;# don't couple langevin bath to hydrogens
> langevinTemp 0 ;#langevin temperature is
>
> langevinPiston on
> langevinPistonTarget 1.01325 ;# in bar -> 1 atm
> langevinPistonPeriod 200
> langevinPistonDecay 100
> langevinPistonTemp 290
>
> and the heating part is:
> # gradual temp increase
> run 1000
> for { set TEMP 0 } { $TEMP <= 290 } {incr TEMP 1 } {
> langevinTemp $TEMP
> run 1000
> }
>
> Is this right?
>
> I could not understand the heating process from log file. It will be
> really helpful if you reply me. Thanks again.
>
>
> On 5/6/10, muniyamuthu.raviprasad_at_ndsu.edu
> <muniyamuthu.raviprasad_at_ndsu.edu> wrote:
>> 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
>> >
>> >
>>
>>
>>
>
>
> --
> Ipsita Basu
> Research Fellow
> c/o : Dr. Chaitali Mukhopadhyay
> Rajabazar Science College
> 92 APC Road
> Kolkata - 700009
>
>

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