Hi,
> in the (Input file preparation) section, Thomas Steinbrecher said "
> Two different ligand transformations need to be simulated, benzene to
> phenol in water and bound to lysozyme".
> but in the table
>
>
> Process 0 (V0) prmtop: t4_bnz prmtop: t4_bnz
> prmtop: t4_phn
> ___________________________________________________________________________
>
> Process 1 (V1) prmtop: t4_bnz prmtop: t4_phn
> prmtop: t4_phn
>
This is only part of the table. The complete one show the prmtops (and
other settings) for the three substeps of the complex-transformation (a
similar table applies for the transformation in water).
The prmtops used are:
Process Step 1 Step 2 Step 3
V0 t4_bnz t4_bnz t4_phn
V1 t4_bnz t4_phn t4_phn
note that Processes V0 and V1 together belong to a single transformation.
Only step 2 actually changes the prmtop file, Steps 1 and 3 only change
charges within a fixed topology.
> 2) I know that in free energy, Zero lambda corresponds to the
> unperturbed system (or the first of the two multisander groups) and
> lambda = 1 corresponds to the perturbed Hamiltonian, or the second of
> the two multisander groups.
>
> what is mean of 0 and 1 in the table above?
The same, but there are three substeps, each with its own V0 and V1. All
three together give the complete transformation.
> 3)Thomas Steinbrecher said "a total of 2 transformations, with 3
> substeps each, with 9 &lambda windows each with 3 simulations each
> will be performed for a total of 162 invocations of the sander module
> (each using at least two CPUs)"
>
> my impression is that I should use 162 times
>
> mpirun -np 2 $AMBERHOME/exe/sander.MPI -ng 2 -groupfile *.group
yes, that is true, by sander above, I meant using the parallel sander.MPI
with -groupfile which has to be used for TI.
> 4) I want to know what step is this groupfile Thomas Steinbrecher put
> in tutotrial about?
>
> -O -i mdin_min_v0_l1 -o t4_bnz_min_v0_l1.out -p t4_bnz.prm -c
> t4_bnz.rst -r 4_bnz_min_v0_l1.rst
> -O -i mdin_min_v1_l1 -o t4_bnz_min_v1_l1.out -p t4_bnz.prm -c
> t4_bnz.rst -r 4_bnz_min_v1_l1.rst
This looks like step 1, the charge removal on some benzene atoms for the
system in water without protein. The content of the mdin files will show
you what actually changes in the run.
Kind Regards,
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 - 04:30:02 PST
