Hello Rajesh,
Yeah, you can include heating step as well in your input file (as
equilibrating temperature ans pressure simultaneously is not recommended)
and yes you will have to include same TI keyword as you will be using in
minimization, equilibration etc....
I did 2000 steps of minimization (1000 with restraints and 1000 without
restraints), 100 ps of heating, 500 ps of pressure equilibration and 3 ns of
production. Hence I got somewhat satisfactory convergence.
My suggestion will be not to stick to the tutorial values ( as it is just
for guidance and giving there the transformation is really small).
On Thu, Apr 7, 2011 at 3:02 AM, Rajesh Raju
<rajesh.raju.mail.chem.tamu.edu>wrote:
> 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 - 22:30:02 PDT
