Re: temperature stepping during heating

From: Low Soo Mei (
Date: Fri Apr 18 2008 - 04:00:41 CDT

I realize I forgot to add the reference that used minimization steps
between heating steps for their membrane simulations. Her e it is:
Langham AA, Ahmad AS and Kaznessis YN (2008). On the nature of
antimicrobial activity: a model for protegrin-1 pores. JACS

Soo Mei

Low Soo Mei wrote:
> Thanks JC for the reply. Yes the temperature did indeed drop
> significantly from the reinitvels temperature after each minimization,
> and it took longer and longer to recover as the temperature increased
> (from 5 K to 10 K, from 10 K to 15 K). It would probably have taken
> more than the 10,000 steps to recover if I had continued the run in
> this way. So I was concerned and stopped it to enquire here about the
> need for minimization. Thanks again.
> Cheers,
> Soo Mei
> JC Gumbart wrote:
>> The minimization in fact is probably hurting you. Plot your
>> temperature as a function of time. After each minimization, I expect
>> your temp drops significantly and then takes longer than 10,000 steps
>> to get back to the target temp.
>> To be honest, I'm not sure such a procedure is necessary, but
>> certainly not in such small increments. You could try increasing the
>> temperature in 20 degree increments for example. In my experience
>> though, many of us just start simulating at 300 K. Since
>> minimization however cuts the temperature in half, it then takes a
>> couple hundred ps for the thermostat to raise the system back up to
>> 300 K. So that is nearly the same as what you're trying to do anyway!
>> I don't know anymore about the additional commands than what is in
>> the manual.
>> On Apr 15, 2008, at 5:21 AM, Low Soo Mei wrote:
>>> 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 - 15:49:24 CST