Hi,
normal mode calculations are rather memory consuming. For a 5000 atom
system, you already need about 900 MByte of memory.
You have to increase the MAXMEMX variable in the sizes.h file in
$AMBERHOME/src/nmode and then recompile nmode.
Also be aware that the DRMS value given in the mm_pbsa.in file in the
example directory $AMBERHOME/src/mm_pbsa/Examples/04_MMPBSA_Nmode is set
to 0.1 to save computation time for demonstration purposes. For real
applications, this value needs to be set to at least 10^-4 or even
smaller.
Best regards
Holger
>
> I commented out the two lines and now I get only the following message
>
> Use of uninitialized value at /usr/local/amber/amber7-serial-xl/src/mm_pbsa/mm_pbsa_statistics.pm line 1259
>
> And the node output file complains that
>
> Total memory required : 6670798 real words
>
> Total memory avail : 3500000 real words
>
> Total memory required : 51568 integer words
>
> Total memory avail : 4000000 integer words
>
> Maximum nonbond pairs 3948431
> increase the real memory by 3170798 words
>
> How do I change this? I get the same problem with the sample files in the
> /src/mm_pbsa directory.
>
> Thanx,
> Mahadevan
>
> On Wed, 8 Jan 2003, Holger Gohlke wrote:
>
> > Hi,
> >
> > could you tell me what happens if you set NM to zero in the mm_pbsa.in
> > file? Also, you might want to comment the lines "unlink $sanout;" and
> > "unlink $nmodeout;" in the function "calc_NM" in mm_pbsa.pl to get
> > output files which give further information why something goes wrong.
> >
> > Best regards
> >
> > Holger
> >
> > > Hi,
> > >
> > > I get the following error message, which I presume is for the nmode
> > > calculations in module.
> > >
> > > Use of uninitialized value at
> > > /usr/local/amber/amber7-serial-xl/src/mm_pbsa/mm_pbsa_statistics.pm line
> > > 1259.
> > >
> > > No skew or curtosis when zero variance in moment
> > >
> > > Use of uninitialized value at
> > > /usr/local/amber/amber7-serial-xl/src/mm_pbsa/mm_pbsa_statistics.pm line
> > > 1608.
> > >
> > > Use of uninitialized value at
> > > /usr/local/amber/amber7-serial-xl/src/mm_pbsa/mm_pbsa_statistics.pm line
> > > 1596.
> > >
> > > Some of these messages are repeated many times. My system is just an RNA
> > > molecule and I am trying to calculate the free energy. I tried the sample
> > > files in the src/mm_pbsa directory and I get the same messages.
> > >
> > > The values in the statistics.out file are
> > >
> > > # MEAN STD
> > > # =======================
> > > ELE 353.10 37.07
> > > VDW -138.32 9.58
> > > INT 1220.14 20.71
> > > GAS 1434.93 40.30
> > > GBSUR 23.86 0.35
> > > GB -5486.90 27.69
> > > GBSOL -5463.03 27.51
> > > GBELE -5133.80 25.54
> > > GBTOT -4028.11 37.35
> > > TSTRA 0.00 0.00
> > > TSROT 0.00 0.00
> > > TSVIB 0.00 0.00
> > > TSTOT 0.00 0.00
> > >
> > > Thanx in advance,
> > > Mahadevan
> >
> > --
> > +++++++++++++++++++++++++++++++++++++++++++++
> > Dr. Holger Gohlke
> > Dept. of Molecular Biology, TPC15
> > The Scripps Research Institute
> > 10550 N. Torrey Pines Rd.
> > La Jolla CA 92037 USA
> > phone: +1-858-784-9788
> > fax: +1-858-784-8896
> > email: gohlke_at_scripps.edu
> > +++++++++++++++++++++++++++++++++++++++++++++
> >
--
+++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke
Dept. of Molecular Biology, TPC15
The Scripps Research Institute
10550 N. Torrey Pines Rd.
La Jolla CA 92037 USA
phone: +1-858-784-9788
fax: +1-858-784-8896
email: gohlke_at_scripps.edu
+++++++++++++++++++++++++++++++++++++++++++++
Received on Wed Jan 08 2003 - 13:52:31 PST
