Dear Thomas Steinbrecher
Thanks for your reply.
There is some ambiguities for me.
My impression from your reply is that
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
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?
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
I want to know what is order of these parts? 1 2 3 4 5 6? and also, I
want to know what is difference between step 1 and 4 or step 2 and 5
or step 3 and 6?
Best regards.
On 11/30/11, steinbrt.rci.rutgers.edu <steinbrt.rci.rutgers.edu> wrote:
> 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
>
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Atila Petrosian
Ph.D. student of BioPhysical Chemistry
University of Oulu,Finland
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Received on Wed Nov 30 2011 - 06:00:08 PST
