Re: error : atom moving too fast

From: muniyamuthu.raviprasad_at_ndsu.edu
Date: Wed May 19 2010 - 09:40:00 CDT

> No I have sent you the complete input file, is there anything missing?

In that case, look at your LangivinTemp and LangvinPistonTemp these two
parameter should be same at every dynamics (your loop does not give that)
I would suggest that you use normal input file (in the manual) instead
script files unless you know scripting very well.
> The charge of my system is 0.
It's OK
> Ok I will check the size of my system after minimization , probably it
> would help.
> One thing I want to know, it is not desired to change the size of my
> system during the run, then if there is any special command to
> maintain my structure.
There is no special command to do that.
You have to use slightly higher values than the size of the model in the
cell basis vector [ Ex: say size of the model is 21.7 50.8 42.9 in X Y Z
respectively, then Cell basis vector may be 23 52 44 ]

> Please help. Thank you.
>
> On 5/17/10, muniyamuthu.raviprasad_at_ndsu.edu
> <muniyamuthu.raviprasad_at_ndsu.edu> wrote:
>> I could not imagine your molecular system BUT I assumed that your system
>> contains water and others.
>>
>> 1] After the minimization, you have to measure the size of your system
>> according to that you may have to change the cell basis vector for
>> equilibration.
>>
>> 2] check charges of the system
>>
>> 3] I hope you're missing some thing in your input file for
>> minimization.
>> [Your input file looks messy......] If you have input file for your
>> minimization only send me that and Send me your heating input file
>> also
>> after the minimization.
>>
>> 4] If it is OK for you to send me your structure file and coordinate
>> file,
>> I will run the model and I can look into that!
>>
>>
>>
>> Ravi
>> ..........................................................
>>
>>
>> > Thank you very much for your freply.
>> > But my problem is whatever input I use, the structure has perfect at
>> > the heating stage, but during equilibration, the structure become
>> > distorted, specifically of water layer, some water molecules are like
>> > to leave the system, and thus the top view of water layer is like
>> > circle rather than a square. I am observing this for a long time .
>> Can
>> > you please suggest me how to maintain the proper bilayer structure. I
>> > am sending you my input file.
>> >
>> > Please tell me what is the reason behind this.
>> > As there is no problem during heating shoul I change the heating
>> > portion of the script. Thanks again.
>> > On 5/15/10, muniyamuthu.raviprasad_at_ndsu.edu
>> > <muniyamuthu.raviprasad_at_ndsu.edu> wrote:
>> >> 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
>> >> >
>> >> >
>> >>
>> >>
>> >>
>> >
>> >
>> > --
>> > 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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