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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