temperature stepping during heating

From: Low Soo Mei (lowsm_at_bii.a-star.edu.sg)
Date: Tue Apr 15 2008 - 05:21:43 CDT


I have a minimized membrane and am now heating it in steps up till 450
K, in NVT, to randomize the lipid tails. A few atoms of my lipid
headgroup are lightly constrained throughout. I'm doing the heating
very cautiously in 5 K steps, with 1000 steps minimization between each
temperature step. This is taking a very long time. Would anyone here
know if the in-between minimization steps are necessary, or if I can use
a bigger temperature step?

The last part of my config file is as below:

# run one step to get into scripting mode
minimize 0

for {set i 5} {$i < 455} {incr i 5} {
set temperature $i
langevinTemp $temperature
run 10000
output heat_flash.$temperature
minimize 1000
output heat_flash.$temperature.min
reinitvels $temperature

As you can see, after each minimization I am using reinitvels to give
back the pre-minimization temperature to my system so that it will not
restart at 0 K. I was also wondering what the differences are between
this (reinitvels) and the temperature rescaling and temperature
reassignment commands in the NAMD user guide.


Soo Mei

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