AMBER Archive (2004)

Subject: AMBER: gibbs calculation

From: Carsten Detering (detering_at_u.washington.edu)
Date: Tue Apr 06 2004 - 13:11:55 CDT

Dear Ambers,

I am using gibbs to calculate thermodynamic integration of a ligand in
the active site, changing a methyl group into an NH2 group.
The minimization/equlibration step semms to have gone fine, but in the
gibbs run, I get

  WARNING: Atom # 15978 more than 1 box length from the central box image.
  WARNING: Atom # 15978 more than 1 box length from the central box image.
  WARNING: Atom # 15979 more than 1 box length from the central box image.
  WARNING: Atom # 15999 more than 1 box length from the central box image.
  WARNING: Atom # 15999 more than 1 box length from the central box image.
  WARNING: Atom # 16000 more than 1 box length from the central box image.
  WARNING: Atom # 16185 more than 1 box length from the central box image.
  WARNING: Atom # 16185 more than 1 box length from the central box image.
  WARNING: Atom # 16186 more than 1 box length from the central box image.
  WARNING: Atom # 16284 more than 1 box length from the central box image.

This is my gibbs input file:
gibbs input, namelist format
  &cntrl
   ntx = 1,
   ntb = 2,
   ntp = 1,
   ntt = 5,
   temp0 = 300.0,
   dt = 0.001,
   nstlim = 1000,
   nstmeq = 300,
   nstmul = 700,

   intprt=1,
   idifrg = 1
   nsnb = 5, cut = 9.,
   scee= 2.0, scnb = 1.23
   ntpr = 50,
   nrun = 11,
   almda = 0.0,
   almdel = 0.1,
   isldyn = -3,
   ielper = 0,

I have been checking in the mail reflector and used the iwrap =1 already
in the MD before using gibbs.
This was my input for the MD run before:

&cntrl

imin = 0

irest = 0

nstlim = 5000

dt = 0.001
iwrap = 1
ntx = 1
ntxo = 1

ntt =1,temp0 = 300.0
ntb = 2, ntp = 1

ntpr = 1

ntwx = 50
ntc = 2
&end

(I had used a longer produnction run without iwrap *before* this one -
do I need to run it longer with iwrap?)

Does anyone have an idea what else to try?

Thanks in advance,

Carsten 

--
Carsten Detering
University of Washington
Seattle, WA 98195
Fon 206.543.5081
Fax 206.685.8665

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