Re: error : atom moving too fast

From: ipsita basu (ibasu788_at_gmail.com)
Date: Fri Jun 11 2010 - 00:19:15 CDT

Can anyone please tell me that the distortion of shape of bilyer
system specifically water portion is mainly due to the wrong value of
cell-dimension vector? Please suggest.

On 6/8/10, ipsita basu <ibasu788_at_gmail.com> wrote:
> ---------- Forwarded message ----------
> From: ipsita basu <ibasu788_at_gmail.com>
> Date: Jun 7, 2010 10:51 AM
> Subject: Re: namd-l: error : atom moving too fast
> To: "m.raviprasad_at_ndsu.edu" <m.raviprasad_at_ndsu.edu>
>
>
> Thank you for your reply.
> My system is distorted again. The structure seems perfect along x
> axis. But If I see it through y axis, then the water molecules are
> totally distorted, the water molecules near bilayer is streached and
> rest are compressed. I am using the pbc cell size given below:
> cellBasisVector1 73.00 00.00 00.00
> cellBasisVector2 00.00 76.00 00.00
> cellBasisVector3 00.00 00.00 95.00
>
> original dimension is
> x = 72.27
> y = 75.29
> z = 95.5
> Will you please suggest me if wrong pbc dimension is the reason, what
> pbc cell size should I use, actually this structure is disturbing from
> a long time although the log file has no problem.
> I am eagerly waiting for your reply as this is really important. Thank
> you very much.
>
> On 6/2/10, m.raviprasad_at_ndsu.edu <m.raviprasad_at_ndsu.edu> wrote:
> > Equilibration is to initialize the system.
> > run script is to do the job by writing codes.
> >
> >
> > In your run script, you have to run for long time in order to achieve
> > equilibration. So, instead of smaller steps (run 1000) you use higher
> > number of steps ( run 50000 or more).
> >
> >
> >
> >
> > > Thank you, I can understand what you said. I have another system which I
> > equilibrated according to your suggestions and that system has no prblem
> > at all. So I think there is another problem in this particular system,
> > and I'll try to solve it.
> > >
> > > I have a question to you after equilibration I want to do long time
> > simulation run on the system, then what is the difference between
> > equilibration and run script as I could not find any. If you will help
> > me it will be really helpful to me. Thanks again.
> > >
> > > On 5/24/10, m.raviprasad_at_ndsu.edu <m.raviprasad_at_ndsu.edu> wrote:
> > >> > I follow your suggestion, but the same thing occures after running
> > >> some
> > >> time, the water molecules are just leaving the system and the
> > structure
> > >> is distorted, there is only problem in the water molecules, not in
> > bilayer or not in protein.
> > >> > You said that my langevin temp and langevin piston temp are not same
> > >> which must be same, I fix langevin temp to 0 as I am heating the
> > system
> > >> to raise the temp of the system from 0 to 298, and that's why I fix
> > piston temp to 298. Is this is the reason?
> > >> langevin temp controls the system temperature. you can not keep that
> > in
> > >> to
> > >> 0 K. you have to write script by considering the langevin temp as a
> > variable.
> > >> Please tell me what
> > >> > should be the langevin temp and lengevin piston temp.
> > >> langevin temp controls the system temperature
> > >> lengevin piston temp maintains the langevin temp during the pressure
> > >> control
> > >> I have trouble
> > >> > for a long time for this problem. Please help me. Thank you very
> > >> much.
> > >> >
> > >> > On 5/19/10, muniyamuthu.raviprasad_at_ndsu.edu
> > >> > <muniyamuthu.raviprasad_at_ndsu.edu> wrote:
> > >> >> > 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
> > >> >> >
> > >> >> >
> > >> >
> > >> >
> > >> > --
> > >> > 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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