Re: slow heating md

From: poker_at_physics.usyd.edu.au
Date: Thu Jun 23 2011 - 20:00:54 CDT

I've been trialling an NPT version of the what you're looking for:
  - it minimises and heats the bath in a number of rounds
  - keeps the total simulation time-steps as a neat number for future
coding and sorting (I believe 9.95 ns of actual simulation time is
roughly equivalent to 10 ns of simulation time given MD's sampling
efficiency).

set init 1
set temperature 300
..(insert NPT controls here)
set tstep 500000 ;# 1000 ps total time

if {$init == 1} {
   set mstep 1500 ;# timesteps of minimisation
   set rounds 10 ;# fraction of final temperature added per round.
   set hstep 2500 ;# timesteps for each round of heating
   set tstep [expr $tstep - ($rounds-1)*$hstep - $mstep]
   minimize $mstep
   for {set i 1} {$i < $rounds} {incr i} {
     set temp [expr $temperature*$i/$rounds.]
     langevinPistonTemp $temp
     langevinTemp $temp
     run $hstep
   }
   langevinPistonTemp $temperature
   langevinTemp $temperature
}
run $tstep

By the way, the NAMD config file *is* a basic TcL script so you can
add a bit of coding.

- Poker.

Quoting Ajasja Ljubeti? <ajasja.ljubetic_at_gmail.com>:

> Have you checked the mailing list archives before posting?
>
> An example can be found here
> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/13613.html
>
> Regards,
> Ajasja
>
> On Thu, Jun 23, 2011 at 13:11, Hasan haska <hasanhaska_at_yahoo.com> wrote:
>
>> Dear NAMD users,
>>
>> I want to make a slow heating md run in NVT from 0K to 300K in increments
>> of 25K every 2ps. How can I do it in conf file ? Can you help me and send an
>> example conf file for this issue ?
>>
>>
>> Thanks a lot.
>>
>

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