AMBER Archive (2006)

Subject: RE: AMBER: Error in running MD in sander

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Sat Jul 08 2006 - 12:38:15 CDT

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_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Gobind Bisht
Sent: Saturday, July 08, 2006 10:20
To: amber_at_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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