AMBER Archive (2008)

Subject: AMBER: Initial Equilibration

From: dpandit_at_brandeis.edu
Date: Thu Apr 10 2008 - 15:45:01 CDT

Hi All:
        I performed initial equilibration using following input. The
main points are protein was restrained using weak force 5 kcal/mol A2.
  I set initial temperature of 0K and set final temperature as 310K
and it was 20PS run. When I checked the output of 20PS equilibration
the temperature reaches only about 300K. Should I extend this
equilibration step further before continuing to whole system
equilibration without restraint. If I extend I feel I could use the
last rst file as a starting point of extended equilibration or do you
think it is better to submit a new equilibration job of ~40 PS.

Input:

Stage 1 - Initial Equilibration/Heating From 0 K to 310 K - Protein
Fixed - 20ps MD
  &cntrl imin = 0,
   irest = 0,
   ntx = 1,
   ntb = 1,
   cut = 10,
   ntr = 1,
   ntc = 2,
   tempi = 0.0
   tempo = 310.0,
   ntt = 3,
   gamma_ln = 1.0,
   nstlim = 10000,
   dt = 0.002
   ntpr = 100, ntwx = 100, ntwr = 1000,
   restraint_wt = 5.0,
   restraintmask=' :1 - 190',
  /

Selected output:

Time Temperature

19.000 302.25
19.200 304.52
19.400 301.73
19.600 303.44
19.800 300.40
20.000 303.23

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