Dear all
I study TUTORIAL A9: (Thermodynamic Integration using soft core potentials).
I have some questions about that:
1) In the page
http://ambermd.org/tutorials/advanced/tutorial9/setup.html
Thomas Steinbrecher mentioned to 4 pdb, prm and rst files:
complex(lysozyme + benzen) - ligand(benzen in water) - t4_phn(lysosyme
+ phenol) - phn(phenol in water).
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
I think following table is true.
Process 0 (V0) prmtop: t4_bnz prmtop: t4_bnz
prmtop: t4_phn
transformation of the
t4_bnz to t4_phn
___________________________________________________________________________
Process 1 (V1) prmtop: bnz prmtop: bnz
prmtop: phn
transformation of the
bnz to phn
please explain this table more.
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?
according to my Knowledge, It should be
transformation of the t4_bnz (0) to t4_phn (1)
transformation of the bnz (0) to phn (1)
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
is it true?
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
--
Atila Petrosian
Ph.D. student of BioPhysical Chemistry
University of Oulu,Finland
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Received on Tue Nov 29 2011 - 07:00:08 PST
