From: ipsita basu (ibasu788_at_gmail.com)
Date: Fri May 14 2010 - 00:14:30 CDT
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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