Dear Case
Thanks for your attention.
I tried with icfe=0
input file:
free_1_eq_v1
&cntrl
imin = 0, ntx = 1, irest = 0,
ntpr = 2500, ntwr = 2500, ntwx = 0,
ntf = 2, ntc = 2,
ntb = 2, cut = 10.0,
nstlim = 250000, dt = 0.002,
temp0 = 300.0, ntt = 3, gamma_ln = 5,
ntp = 1, pres0 = 1.0, taup = 0.2,
/
Again, the job stopped, in NSTEP = 1.
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
| # of SOLUTE degrees of freedom (RNDFP): 46649.
| # of SOLVENT degrees of freedom (RNDFS): 0.
127,0-1
15%
| # of SOLUTE degrees of freedom (RNDFP): 46649.
| # of SOLVENT degrees of freedom (RNDFS): 0.
| NDFMIN = 46649. NUM_NOSHAKE = 0 CORRECTED RNDFP = 46649.
| TOTAL # of degrees of freedom (RNDF) = 46649.
---------------------------------------------------
APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
using 5000.0 points per unit in tabled values
TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
| CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
| CHECK d/dx switch(x): max rel err = 0.8314E-11 at 2.736960
---------------------------------------------------
| Local SIZE OF NONBOND LIST = 1781578
| TOTAL SIZE OF NONBOND LIST = 6626689
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
-6152.6
Etot = -69128.0749 EKtot = 0.0000 EPtot =
-69128.0749
BOND = 43.5638 ANGLE = 284.9209 DIHED =
548.3179
1-4 NB = 256.3398 1-4 EEL = -2197.0692 VDWAALS =
4338.2557
EELEC = -72402.4039 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 0.0000 VIRIAL = 39664.4653 VOLUME =
298583.2222
Density =
0.7884
Ewald error estimate: 0.9305E-03
------------------------------------------------------------------------------
NSTEP = 1 TIME(PS) = 0.002 TEMP(K) = 6.28 PRESS =
-6152.1
Etot = -68837.0169 EKtot = 291.0580 EPtot =
-69128.0749
BOND = 43.5638 ANGLE = 284.9209 DIHED =
548.3179
1-4 NB = 256.3398 1-4 EEL = -2197.0692 VDWAALS =
4338.2557
EELEC = -72402.4039 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 3.3747 VIRIAL = 39664.4653 VOLUME =
298583.2222
Density =
0.7884
Ewald error estimate: 0.9305E-03
------------------------------------------------------------------------------
I tried to do jobs being in tutorial A6. They run without problem.
Please guide me to resolve it.
On Mon, Feb 13, 2012 at 6:15 AM, case <case.biomaps.rutgers.edu> wrote:
> On Sun, Feb 12, 2012, leila karami wrote:
> >
> > Try a standard run (with ifce=0). what is yor mean? icfe?
>
> Yes, I meant icfe.
> >
> > When I use nstlim=10, ntpr=1 in input files, job stopped in NSTEP=2.
>
> It is not obvious why your job is stopping after two steps. So you need to
> run as many (short) experiments as you can. Try with icfe=0; try using
> just
> two threads (mpirun -np 2). Of course, but sure you are passing the
> parallel
> tests (especially those in $AMBERHOME/test/ti_ggcc, for example). Look at
> the
> ti_ggcc test case, and see if you can spot any differences between what you
> are doing and those test cases.
>
> Debugging is mainly a procedure to try to narrow down the cause of the
> problem.
>
> ...good luck...dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Feb 13 2012 - 02:30:02 PST
