AMBER Archive (2002)

Subject: DNA Tutorial: min_ntr.in

From: Joel Konkle-Parker (joelkp_at_ERC.MsState.Edu)
Date: Fri Oct 11 2002 - 17:28:47 CDT

I am trying to understand the input file min_ntr.in found in the third
section of the DNA tutorial
(http://sigyn.compchem.ucsf.edu/amber/tutorial/polyA-polyT/equilibration.html).
In particular, you've changed the default values of a few of Sander's
input parameters, and I'm wondering why.

The parameters are: dx0, nscm, ntt, and tautp

It should be noted that instead of running the same minimization as the
tutorial (simplified solvated molecule for shorter run time, etc.), I'm
using the original polyAT set from earlier in the tutorial. As such,
I've turned off SHAKE (ntc, ntf) and set ncyc = 500.

Can you explain these changes for me?

-Joel