AMBER Archive (2006)

Subject: AMBER: Error in running MD in sander

From: Gobind Bisht (gsbisht1_at_gmail.com)
Date: Sat Jul 08 2006 - 12:20:10 CDT

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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