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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> >
>
>
>
>
> --
> SUNITA GUPTA
>
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>
>
--
Manikanthan Bhavaraju
Graduate Teaching Assistant
Dept. of Chemistry
Mississippi State University
office no : 662-325-4633
MS -39762
USA.
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Received on Mon May 24 2010 - 18:00:06 PDT
