Dear amber users
I'm beginner in amber.
I study tutorial A6 (pKa Calculations Using Thermodynamic Integration).
I have a question about section2 : Run thermodynamic integration on the
model compound to find delta-G(model).
I use amber 10 and in my system, cpu cores : 2. thus I don't use
mpirun -np 2 $AMBERHOME/exe/sander.MPI -ng 2 -groupfile model_step1.group.
Instead, I used
$AMBERHOME/bin/sander -O -i model_step1.mdin -p asph_model.prmtop -c
asph_model.inpcrd -o asph_model_step1.out
-inf asph.mdinfo -x asph_model_step1.mdcrd -r asph_model_step1.rst -O -i
model_step1.mdin -p asp_model.prmtop
-c asp_model.inpcrd -o asp_model_step1.out -inf asp.mdinfo -x
asp_model_step1.m
after using sander, 2 out files (asp_model_step1.out and
asph_model_step1.out) were created.
but in CONTROL DATA FOR THE RUN section:
in my output:
SHAKE:
ntc = 2, jfastw = 0
tol = 0.00001
*numgroup must be 2 if icfe is set*
in tutorial output:
SHAKE:
ntc = 2, jfastw = 0
tol = 0.00001
*Free energy options:
icfe = 1
klambda = 1
clambda = 0.00000*
how to fix it?
please guide me about that.
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Received on Sun Oct 30 2011 - 03:30:03 PDT
