Re: AW: Tcl script for simulated tempering?

From: Brian Radak (bradak_at_anl.gov)
Date: Tue Mar 15 2016 - 08:14:11 CDT

Thanks for the reply - yes, that is definitely the main point.
Unfortunately you described simulated /annealing/, whereas I want
simulated /tempering/. Pointless semantics distinction? Probably.

Essentially I want to run hybrid MD/MC with the temperature changing
along a fixed ladder using set statistical weights. I mostly just want
to get a little bit better convergence out of some small alchemical
calculations where some torsional barriers are rather important - and of
course I want to avoid scaling this up to many many replicas in order to
avoid a nail/sledge hammer situation.

Ultimately my main problem is that I'm not yet familiar with the
specific ways that one can interact with the NAMD data (e.g. energy,
volume) within Tcl. I can infer some of this from the parallel tempering
(temperature replica exchange) script, but there's a lot of extra
indexing, etc. in that example that I definitely do not need.

Cheers,
Brian

On 03/15/2016 02:53 AM, Norman Geist wrote:
>
> For this purpose, you’d just need to understand that the namd inout
> script, is in fact a TCL script. So just leave out the numsteps
> parameter and do something like the following at the end of your namd
> conf:
>
> […]
>
> set startT 10
>
> set endT 300
>
> set stepT 10
>
> set perrun 1000000
>
> set runs [expr floor(($endT-startT)/stepT)]
>
> for {set i 0} {$i < $runs} {incr i} {
>
> langevintemp [expr $startT+($i*$stepT)]
>
> run $perrun
>
> }
>
> Norman Geist
>
> *Von:*owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *Im
> Auftrag von *Radak, Brian K
> *Gesendet:* Freitag, 11. März 2016 23:12
> *An:* NAMD list ‎[namd-l_at_ks.uiuc.edu]‎ <namd-l_at_ks.uiuc.edu>
> *Betreff:* namd-l: Tcl script for simulated tempering?
>
> Has anyone implemented a generic Tcl script for simulated tempering? I
> know that I could probably cannibalize the parallel tempering script
> for this purpose, but I'm not one to re-invent the wheel.
>
> Thanks,
> Brian
>
> Brian Radak
> Postdoctoral Appointee
> Leadership Computing Facility
> Argonne National Laboratory
>
> 9700 South Cass Avenue, Bldg. 240
> Argonne, IL 60439-4854
> (630) 252-8643
> brian.radak_at_anl.gov <mailto:brian.radak_at_anl.gov>
>

-- 
Brian Radak
Postdoctoral Appointee
Leadership Computing Facility
Argonne National Laboratory
9700 South Cass Avenue, Bldg. 240
Argonne, IL 60439-4854
(630) 252-8643
brian.radak_at_anl.gov

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