Re: error : atom moving too fast

From: ipsita basu (ibasu788_at_gmail.com)
Date: Mon Jun 14 2010 - 01:52:37 CDT

Thank you for your reply.
I have another thing to know, I want to apply restraints on lipids and
water molecules too, so what will be the tcl script for that.
I use the below script by which only the protein backbone is restrained:
set all [atomselect top all]
set sel [atomselect top "protein and backbone"]
$all set beta 0
$sel set beta 0.5
$all writepdb restrain_ca.pdb

Should I change the value of $all set beta 0 to $all set beta 1.0 ?

Please help.

On 6/11/10, francesco oteri <francesco.oteri_at_gmail.com> wrote:
> Yes, it is possible. To be sure, put the exact values ( i.e.
> cellBasisVector1 72.27 00.00 00.00
> cellBasisVector2 00.00 75.29 00.00
> cellBasisVector3 00.00 00.00 95.5
>
> )
>
> 2010/6/11 ipsita basu <ibasu788_at_gmail.com>
>
> > 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
> >
> >
>
>
>
> --
> Cordiali saluti, Dr.Oteri Francesco
>

-- 
Ipsita Basu
Research Fellow
c/o : Dr. Chaitali Mukhopadhyay
Rajabazar Science College
92 APC Road
Kolkata - 700009

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