Hi,
> 1) Table in tutorial relates to only one of two transformation you
> mentioned (transformation of the benzene bound to lysozyme). And table
> relating to the transformation of the benzene in water is as follows:
>
> Process Step 1 Step 2 Step 3
> V0 bnz bnz phn
> V1 bnz phn phn
that is correct. The mask, ifsc, crgmask settings stay the same as in the
complex for the in-water transformation.
> 2) I should use 162 times mpirun -np 2 $AMBERHOME/exe/sander.MPI -ng 2
> -groupfile *.group for the transformation of the benzene bound to
> lysozyme and 162 times for the transformation of the benzene in water.
> Is it true?
You do 2 transformations (in complex and in water) x 3 substeps (charges,
vdW, charges again) x 9 lambdas x three runs (minimization, equilibration,
production) so a total of 162 calls to mpirun. The total number is not
important, e.g. the minimization runs are much shorter than the
productions and a real study would look different anyway.
> 3) Unfortunately, table in tutorial is unclear for me.
>
> Your table (benzene to phenol transformation in bound state) contain 6
> parts
>
> 1 2 3
> __________________
>
> 4 5 6
1 and 4 are both settings used in step 1 (charge removal). The substep
uses two different mdin-files. The same goes for 2+5 and 3+6. The overall
transformation you want is 1->6 but you do it in substeps 1->4 2->5 and
3->6 and add their results together.
If you study the prepare_example.bat script that comes with the tutorial
you will see how the different steps/program calls/input files are all put
together for the complete run.
Thomas
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Wed Nov 30 2011 - 08:30:04 PST
