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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Received on Fri Apr 18 2008 - 21:18:26 PDT
