Ross,
> Sorry I can't offer much more help than that. - Note you could also try
> cut=0.001 and see if that works. There is almost certainly a 1.0d0/cut^2
> somewhere in the code and this might work around that and still give you
> what you want from the simulation.
I tested sander12 with cut = 0.1, same type of crash; so this is not a
problem of division by zero...
see below the end of the sander output.
regards, Francois
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
| # of SOLUTE degrees of freedom (RNDFP): 24936.
| # of SOLVENT degrees of freedom (RNDFS): 0.
| NDFMIN = 24933. NUM_NOSHAKE = 0 CORRECTED RNDFP = 24933.
| TOTAL # of degrees of freedom (RNDF) = 24933.
---------------------------------------------------
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 = 0.8987E-11 at 2.875760
---------------------------------------------------
| Local SIZE OF NONBOND LIST = 25
| TOTAL SIZE OF NONBOND LIST = 123
---> crash
>
> On 2/23/14, 9:19 AM, "FyD" <fyd.q4md-forcefieldtools.org> wrote:
>
>> Dear All,
>>
>> I ran amber10/sander.MPI with PME + cutoff = 0 -> sander crashes
>> amber12/sander.MPI with PME + cutoff = 0 -> sander crashes
>> (compiled with intel13 + mkl)
>> amber12/pmemd.MPI with PME + cutoff = 0 -> pmemd does not crash...
>>
>> Printed output: printing stops in section 4:
>>
>> --------------------------------------------------------------------------
>> ------
>> 4. RESULTS
>> --------------------------------------------------------------------------
>> ------
>>
>> | # of SOLUTE degrees of freedom (RNDFP): 24936.
>> | # of SOLVENT degrees of freedom (RNDFS): 0.
>> | NDFMIN = 24933. NUM_NOSHAKE = 0 CORRECTED RNDFP =
>> 24933.
>> | TOTAL # of degrees of freedom (RNDF) = 24933.
>>
>> -> nothing else is printed...
>>
>> In Fox & Kollman J.Phys.Chem.B 1998, 102, 8070, MD simulation with
>> cutoff = 0 is reported & Sander from Amber 4.1 was used.
>>
>> Why does sander crash, while pmemd does not crash in this case?
>> (with the same input & cut = 12, sander does not crash)
>>
>> thank you, regards,
>> Francois
>>
>>
>>
>> # Cst pressure simulation with cutoff = 0 Angs; 300 K short
>> $PARAL -np $NPROC $EXE -O -i md-cstpres0.in \
>> -o md-cstpres0b.out \
>> -p $mol.parm7 \
>> -c md-cstvol.rst7 \
>> -r md-cstpres0b.rst7 \
>> -x md-cstpres0b.mdcrd
>>
>> my test input below:
>>
>> cst pressure MD, nstlim*dt psec, PME with cutoff
>> &cntrl
>> nmropt = 0, ioutfm = 1, iwrap = 0,
>> ntx = 1, irest = 0, ntrx = 1, ntxo = 1,
>> ntpr = 100, ntwr = 1000, ntwx = 500,
>> ntave = 0, ntwv = 0, ntwe = 0,
>> ntf = 2, ntb = 2,
>> ntc = 2, tol = 0.00001,
>> dielc = 1, ipol = 0,
>> cut = 0, ig = 71277, comp = 52.5,
>> ibelly = 0, ntr = 0, igb = 0,
>> imin = 0, nstlim = 5000,
>> nscm = 1000, t = 0.0, dt = 0.002,
>> temp0 = 300, tempi = 300,
>> ntt = 1, tautp = 0.2, vlimit = 20,
>> ntp = 1, pres0 = 1.0, taup = 0.2,
>> &end
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Feb 24 2014 - 05:00:04 PST
