Dear Gobind,
You don't have enough memory to run this calculation. Your simulation is for
a system with 278335 atoms and you are running it in gas phase with no
periodic boundaries and a 16 angstrom cut off. You really should stop and
think whether this really is what you want to do. Remember proteins do not
exist in a vacuum so simulating them in a vacuum is unlikely to tell you
much. Also you should remember that anything over about 100,000 atoms is
considered a BIG system and this is for a system in explicit solvent with
PME and an 8 angstrom cut off. You want to run a system almost 3 times as
big with a 16 angstrom cutoff!!! At best on a single processor machine under
cygwin you can probably hope for maybe half a picosecond a day if you are
lucky. Really a system this big would require a supercomputer wth 64 cpus or
more to have any hope of getting a useful amount of simulation done.
Although again if this is a protein in vacuum even then you would be largely
wasting your time.
All the best
Ross
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From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Gobind Bisht
Sent: Saturday, July 08, 2006 10:20
To: amber.scripps.edu
Subject: AMBER: Error in running MD in sander
Hi all,
i am running md simulations my molecule. BUt the following error
message was generated by sander in md.out file:
Here is the input file:
Initial MD simulation for atpase+adp
&cntrl
imin=0, irest=0,
nstlim=20000,dt=0.001, ntc=2,
ntpr=100, ntwx=100,
cut=16, ntb=0, igb=0,
ntt=3, gamma_ln=2.0,
tempi=300.0, temp0=300.0,
/
----------------------------------------------------------------------------
----
1. RESOURCE USE:
----------------------------------------------------------------------------
----
| Flags:
| NONPERIODIC ntb=0 and igb=0: Setting up nonperiodic simulation
|Largest sphere to fit in unit cell has radius = 96.041
| New format PARM file being parsed.
| Version = 1.000 Date = 07/08/06 Time = 04:03:44
NATOM = 278335 NTYPES = 21 NBONH = 253674 MBONA = 24977
NTHETH = 57073 MTHETA = 33827 NPHIH = 107156 MPHIA = 66222
NHPARM = 0 NPARM = 0 NNB = 579152 NRES = 79460
NBONA = 24977 NTHETA = 33827 NPHIA = 66222 NUMBND = 60
NUMANG = 125 NPTRA = 61 NATYP = 42 NPHB = 1
IFBOX = 1 NMXRS = 43 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Memory Use Allocated
| Real 13365138
| Hollerith 1749472
| Integer 9544970
| Max Pairs 541083240
ASSERTion ' ier == 0 ' failed in sander.f at line 223.
Th configuration of my windows machine (using cygwin to run amber) is :
3Ghz, 1 GB ram
could any one help please.......
--
Gobind Singh Bisht
Department Of Biotechnology
IIT Kharagpur, Kharagpur-721302
West Bengal,India
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Received on Sun Jul 09 2006 - 06:07:26 PDT
