RE: AMBER: AMBER minimization problems

From: Ross Walker <ross.rosswalker.co.uk>
Date: Wed, 17 Dec 2008 08:18:06 -0800

Hi Lili,

 

What do you mean by 'ends'? Do you get any further output? Any error
messages of any kind? It would also be helpful to see your input file.

 

All the best

Ross

 

From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Lili Peng
Sent: Tuesday, December 16, 2008 11:14 PM
To: amber.scripps.edu
Subject: AMBER: AMBER minimization problems

 

Hi AMBER,

I'm having trouble minimizing a 5000 Dalton polyethylene glycol molecule
solvated in a TIP3PBOX 15 water molecules. The output file I get ends after
the 2nd nstep of 500 (shown below). This is after I've vacuumed minimized
my molecule (and then solvated it in water). I've attached my water
minimization file input file. Do anyone know what the problem could be?

Thanks,
Lili

---------------------------------------------------------------------------- 
----
   4.  RESULTS
----------------------------------------------------------------------------
----
 ---------------------------------------------------
 APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
 using   5000.0 points per unit in tabled values
 TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
| CHECK switch(x): max rel err =   0.2738E-14   at   2.422500
| CHECK d/dx switch(x): max rel err =   0.8314E-11   at   2.736960
 ---------------------------------------------------
| Local SIZE OF NONBOND LIST =   64267381
| TOTAL SIZE OF NONBOND LIST =  130524253
   NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
      1      -2.0703E+06     1.2881E+01     4.6850E+01     O      255159
 BOND    =       16.4676  ANGLE   =        8.8005  DIHED      =
158.2966
 VDWAALS =   255110.9185  EEL     = -2325481.7410  HBOND      =
0.0000
 1-4 VDW =      105.8433  1-4 EEL =     -249.6019  RESTRAINT  =
0.0000
   NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
    500      -2.6528E+06     9.0587E-01     4.5299E+00     H1     309256
 BOND    =   182580.9181  ANGLE   =        4.6033  DIHED      =
157.3146
 VDWAALS =   382897.9872  EEL     = -3218340.8995  HBOND      =
0.0000
 1-4 VDW =      103.2430  1-4 EEL =     -249.2364  RESTRAINT  =
3.5502
 EAMBER  = -2652846.0697
 
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Received on Fri Dec 19 2008 - 01:09:22 PST
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