Dear Amber Users,
I am trying to do Thermodynamic interaction for a DNA-protein system.
I want to performance TI by changing one of the TYR to Phe. I may also
want to perform TI by changing DNA bases to. Since this is my first TI
calcution, I referred the amber tutorials titled TUTORIAL A9:
Thermodynamic Integration using soft core potentials....I have some
doubts regarding the input file section. the copy pasted part of the
tutorial is given below
[The mdin files used for these transformations contain the normal
Amber parameters for performing Minimizations/MD simulations that I
will not discuss further and in addition to that some unique
parameters to perform the TI calculations. The non-TI parts of the
input files will perform the following steps:
500 steps of steepest descent minimization (the only kind working
with TI)
50 ps of density equilibration (equilibrating T and &delta at the
same time is not very good form, but we'll get away with it here
200 ps of NPT production MD to collect dV/d&lambda data]
My questions:
[1] Should I include heating stage after the
minimization? I could not find a heating stage in the tutorial...
[2] The input file section mentioned in the tutorials
have TI keywords in all steps including both minimization and
equilibration.. So if I include heating stage do I need to include the
TI key words too?
Thanking you in adavance
Rajesh
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Received on Wed Apr 06 2011 - 15:00:03 PDT
