From: ipsita basu (ibasu788_at_gmail.com)
Date: Tue Jun 08 2010 - 00:20:24 CDT
---------- 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
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