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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Received on Mon May 24 2010 - 03:30:08 PDT
