Thermodynamic integration *MUST* be used with the groupfile (and *cannot*
be run in serial). In this case, you can't deviate from the tutorial.
HTH,
Jason
On Sun, Oct 30, 2011 at 6:21 AM, leila karami <karami.leila1.gmail.com>wrote:
> 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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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sun Oct 30 2011 - 10:00:02 PDT
