Ya,after visualizing the mdcrd files of for the lambda values for which the
job is getting crashed, I observed that the ligand is blowing out of the
water box and also the structure of the ligand is destroyed completely.
Also, how can I restart the job using charge annihilation step, as the lamba
values for the two steps are not identical?
For this I thing I will have to setup charge annihilation step for lambda
value 0.56262 and take it further to vdw decoupling step.
Kindly guide me.
On Tue, May 25, 2010 at 6:20 AM, manikanthan bhavaraju <
manikanthanbhavaraju.gmail.com> wrote:
> Hello,
> Did you visualize the mdcrd files for the lambda values for which the job
> is
> getting crashed? Did you see anything unusual during the simulation? As dac
> said try to use the restart of the decharging step.
>
> manikanthan
> On Mon, May 24, 2010 at 5:14 AM, sunita gupta <sunita.bio.gmail.com>
> wrote:
>
> > Hello,
> >
> > I am dealing with solvated ligand system and following these two steps:-
> > 1st. charge annihilation
> > 2nd. vdw decoupling
> >
> > For Charge annihilation I took 0.04691, 0.23076, 0.5, 0.76923, 0.95308
> > lambda values.....and did minimization, heating, equilibration and
> > production and there was no problem with these jobs.
> >
> > Now for vdw decoupling I took 0.00922, 0.04794, 0.11505, 0.20634,
> 0.31608,
> > 0.43738, 0.56262, 0.68392, 0.79366, 0.88495, 0.95206, 0.99078 values of
> > lambda. Here the partial atomic charges were removed and vdw was
> decoupled
> > using softcore potentials.
> > Find the script as attachment (includes minimization to production for
> all
> > lambda values).
> >
> > The lambda values 0.00922 and 0.99078 are not running as its out of the
> > range of 0.01 < clambda < 0.99 (as per manual).
> > Lambda value 0.95206 is crashing at the minimization step only...leading
> to
> > some NaN NaN values...
> >
> > *NSTEP ENERGY RMS GMAX NAME NUMBER
> > 678 NaN NaN 2.5150E+04 C4 5
> > BOND = 969.0638 ANGLE = 0.0000 DIHED =
> > 0.0000
> > VDWAALS = 2171.7619 EEL = NaN HBOND =
> > 0.0000
> > 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT =
> > 0.0000
> > DV/DL = NaN
> > Softcore part of the system: 32 atoms, TEMP(K) =
> > 0.00
> > SC_BOND= *********** SC_ANGLE= 5118.2656 SC_DIHED =
> > 242.5858
> > SC_14NB= -0.2115 SC_14EEL= 0.0000 SC_EKIN =
> > 0.0000
> > SC_VDW = 6.9212 SC_DERIV= -3.0076*
> >
> > And the two lambda values 0.31608 and 0.56262 are crashed during
> > heating....with so many vlimit errors....And after changing these values
> > to
> > 0.3 and 0.5 respectively, they are running fine with the same
> > parameters....
> >
> > No, I have not tried vdW decoupling using the restart files from the end
> of
> > the charge annihilation step. Should I try it?
> > Thanks for you reply
> >
> >
> >
> >
> >
> > On Sun, May 23, 2010 at 9:17 AM, manikanthan bhavaraju <
> > manikanthanbhavaraju.gmail.com> wrote:
> >
> > > Firstly why are heating your system during the TI calculations? Could
> you
> > > give us more details about your equilibration process and TI
> > calculations.
> > >
> > > manikanthan
> > >
> > > On Sat, May 22, 2010 at 7:18 PM, case <case.biomaps.rutgers.edu>
> wrote:
> > >
> > > > On Sat, May 22, 2010, sunita gupta wrote:
> > > > >
> > > > > I am doing TI using AMBER10. I successfully did the charge
> > annihilation
> > > > > step, but while doing vanderwal decoupling my job crashes at some
> > > lambda
> > > > > values.
> > > >
> > > > Can you give some details about your input files? Are you using
> > softcore
> > > > potentials? It is possible that your system is on the edge of
> > > instability
> > > > (especially if you are heating quickly) and you were just lucky
> before.
> > > > Have
> > > > you tried just starting the vdW decoupling using the restart files
> from
> > > the
> > > > end of the charge annihilation step?
> > > >
> > > > [It does seem hard to see how there would be a systematic difference
> > (or
> > > a
> > > > bug) that would lead to results being different for two rather
> similar
> > > > values
> > > > of lambda.]
> > > >
> > > > ....dac
> > > >
> > > >
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > >
> > >
> > >
> > > --
> > > _______________________________________________
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> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> >
> > --
> > SUNITA GUPTA
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
>
> --
> Manikanthan Bhavaraju
> Graduate Teaching Assistant
> Dept. of Chemistry
> Mississippi State University
> office no : 662-325-4633
> MS -39762
> USA.
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>
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Received on Tue May 25 2010 - 00:00:06 PDT
