This is almost certainly a memory issue. Each normal mode calculation can
take a couple of gigabytes of RAM. How many calculations are you attempting
to perform at the same time with the 8 GB of RAM allotted? The memory
required is obviously dependent on the size of the system. This is the
reason you do not see the "allocation failure" error in
_MMPBSA_ligand_nm.out. The ligand is small enough that it does not require
much memory to perform the normal mode calculation. I would suggest using
less threads for the parallel calculation, or use more processors with more
available RAM. With 8 GB of RAM available, I would not do more than probably
2 threads (i.e. mpirun -np -2 MMPBSA.py.MPI) at one time for an
average-sized protein system.
I hope that helps.
-Bill
On Tue, Dec 14, 2010 at 7:11 AM, mish <smncbr.gmail.com> wrote:
> Hi all,
> I tried normal mode calculations in a protein (268 aa long). I used
> parallel
> version of MMPBSA.py.MPI (python script) for calculating the entropy. The
> no
> results written out in FINAL_RESULTS_MMPBSA.dat . following is the output,
> can you please point the possible places where I am doing wrong. The
> _MMPBSA
> _complex_nm.out and _MMPBSA_receptor_nm.out files contain an error
> "allocation failure in vector: nh = 284339701 ", where as
> _MMPBSA_ligand_nm.out
> doesnot have this error. This looks like an memory allocation problem but I
> had also tried the calculations by assigning 8GB of memory and the problem
> still persist. Can any of you point out teh origin of errors in the
> calculations.
>
>
> -----------------FINAL_RESULTS_MMPBSA.dat----------------
>
> | Run on Tue Dec 14 02:33:44 CET 2010
>
> |Input file:
> |--------------------------------------------------------------
> |Input file for running entropy calculations using NMode
> |&general
> | endframe=50, keep_files=2,
> |/
> |&nmode
> |nmstartframe=5, nmendframe=45,
> |nminterval=5, nmode_igb=1, nmode_istrng=0.1,
> |/
> |
> |
> |--------------------------------------------------------------
> |Complex topology file: com.prmtop
> |Receptor topology file: rec.prmtop
> |Ligand topology file: lig.prmtop
> |Initial mdcrd(s): prod.mdcrd
> |
> |Best guess for receptor mask: ":1-266"
> |Best guess for ligand mask: ":267-268"
>
> |Calculations performed using 50 frames.
> |NMODE calculations performed using 9 frames.
> |
> |All units are reported in kcal/mole.
> |All entropy results have units kcal/mole (Temperature is 298.15 K).
>
> -------------------------------------------------------------------------------
>
> -------------------------------------------------------------------------------
> NO NMODE ENTROPY CALCULATED. SNAPSHOTS NOT MINIMIZED!
>
>
> -------------------------------------------------------------------------------
>
> -------------------------------------------------------------------------------
>
>
> ================== _MMPBSA_complex_nm.out
> ====================================
> ----Convergence Satisfied----
>
> iter Total bad vdW elect nonpolar genBorn
> frms
> ff: 1 -1716.85 2410.88 -1792.90 -1732.53 0.00 -602.30
> 9.68e-04
>
> Energy = -1.7168452022e+03
> RMS gradient = 9.6806388713e-04
> allocation failure in vector: nh = 280631737
> Reading parm file (com.prmtop)
>
> ============================================================================
>
>
> Thanking you in advance
>
> .S
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>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Tue Dec 14 2010 - 04:30:03 PST
