temperature stepping during heating

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

Hi,

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.

Thanks!

Cheers,
Soo Mei

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:49:23 CST