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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Received on Tue Apr 06 2004 - 19:53:00 PDT
