AMBER Archive (2003)

Subject: Nmode

From: thenmalar rathinavelan (thenmalrr_at_yahoo.co.in)
Date: Thu Feb 20 2003 - 00:21:03 CST

Dear ambers,
  I have some doubts regarding the usage of Nmode. I
want to compare the free energy of formation of two
DNA systems (1437 atoms). For that, I have done
steepest descent and conjugate gradient minimiztaion
using sander_classic and I am using Nmode for
Newton-Rapson minimization. I have following doubts
regarding this:
 (i) If I have carried out Newton-Rapson minimization
for the convergence of 0.0001, convergence is not
reached even after 18 hours. So, I have changed the
convergence to 0.01 and now I am able to reach the
convergence within 9 hours. If I use the convergence
of 0.01 will it affect the calculation of free-energy?
 (ii) I have used nvec=200, bdwnhl=0.01 and dfpred=0.1
as given in the example file (amber 4.1). Can I use
these values? otherwise how to choose these values.
 (iii) In the manual (Nmode) it is mentioned that
dielc=1 and idiel=0 should be used for r^^2 distance
dependence. But, for minimization (using
sander_classic and also for anal) I have used dielc=4
and idiel=0 for 4rij. My question is that which one
should be used for the calculations - r^^2 distance
dependence or 4rij.(I have used scee=1.2 for all the
calculations, since I am using parm98.dat force field)
 (iv) I have done dynamics for 4ns. Is it sufficient
if I take the last 1.5ns (at 20ps intervals) alone for
the calculation?
 (v) For the calculation of free energy I am using
MM-GBSA. In /amber6/src/mm_pbsa/SOURCS/GB.F file only
the solvent dielectric constant (eps=80) is given and
not the solute dielectric constant (=1). Where should
it be given?
 Kindly, tell your suggestions regarding this.
 Thank you very much.

Thenmalar

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