From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Tue Jan 26 2016 - 08:03:40 CST
The output changed little, but it should still work, but only if column three in the history file does also show something else than “300”. What settings did you use for min_temp and max_temp? Could it be that all your replicas were running at 300K ?? Can you show your *_remd.conf
Norman Geist
Von: Chitrak Gupta [mailto:chgupta_at_mix.wvu.edu]
Gesendet: Montag, 25. Januar 2016 16:59
An: Norman Geist <norman.geist_at_uni-greifswald.de>
Cc: NAMD list <namd-l_at_ks.uiuc.edu>
Betreff: Re: namd-l: calculating replica exchange acceptance ratio
Now I see why I had the confusion before. For some reason, both the temperatures are being shown the same in the output of the pdes.tcl code. I am copy-pasting part of the result here.
EXCHANGE_RATIO 300 300 29 50 0.58
EXCHANGE_RATIO 300 300 25 50 0.5
EXCHANGE_RATIO 300 300 30 50 0.6
EXCHANGE_RATIO 300 300 31 50 0.62
EXCHANGE_RATIO 300 300 23 50 0.46
Shouldn't these temperatures be different?
On Mon, Jan 25, 2016 at 9:21 PM, Chitrak Gupta <chgupta_at_mix.wvu.edu <mailto:chgupta_at_mix.wvu.edu> > wrote:
Hi Norman,
The history file columns look like this
100 0 300 -80595.06905838488
200 1 300 -80394.8947269207
300 1 300 -80396.61219236573
400 0 300 -80633.88125895151
500 0 300 -80446.22636982969
600 0 300 -80231.83412244706
I believe the ordering is Step #, Replica #, Temperature, Energy. Is that what it used to be when you wrote the code?
Also, thanks for the explanation on the temperature. That makes sense now.
Regards,
Chitrak.
On Mon, Jan 25, 2016 at 5:21 PM, Norman Geist <norman.geist_at_uni-greifswald.de <mailto:norman.geist_at_uni-greifswald.de> > wrote:
Well, when I wrote that script, the output it did was identical to the one that replica.namd produced. So I’m sure that the output always printed the temperature, not the replica number, since the temperature->replica_id assignment is not fixed.
Norman Geist
Von: owner-namd-l_at_ks.uiuc.edu <mailto:owner-namd-l_at_ks.uiuc.edu> [mailto:owner-namd-l_at_ks.uiuc.edu <mailto:owner-namd-l_at_ks.uiuc.edu> ] Im Auftrag von Chitrak Gupta
Gesendet: Montag, 25. Januar 2016 09:54
An: Norman Geist <norman.geist_at_uni-greifswald.de <mailto:norman.geist_at_uni-greifswald.de> >
Cc: NAMD list <namd-l_at_ks.uiuc.edu <mailto:namd-l_at_ks.uiuc.edu> >
Betreff: Re: namd-l: calculating replica exchange acceptance ratio
Hi Norman,
Thanks a lot for sending this code.
When I tried it, it kept giving false for the "info exists psf_file", even though I did source job0.conf. I couldn't track it down, could it be because I do not have any variable named psf_file? I have "structure" variable set in the *_base.namd file, which is basically the psf file. I tried changing psf_file to structure, but that didn't help.
I then tried commenting out the first check. This worked, except that now "temp1" and "temp2" are both set to 300 (the target temperature) instead of the replica numbers.
Any clue why this is happening and how I can fix this?
Best regards,
Chitrak.
On Mon, Jan 25, 2016 at 2:13 AM, Norman Geist < <mailto:norman.geist_at_uni-greifswald.de> norman.geist_at_uni-greifswald.de> wrote:
# Reconstruct exchange ratio information from replica history files
# by Norman Geist 2013
set go 1
if {! [info exists psf_file] } {
puts "Error: You forgot to source the job.conf"
set go 0
}
if { $go } {
if {! [info exists i_job]} { set i_job 0 }
set outputbase "$output_root.job$i_job"
set history_filename_format "${outputbase}.%d.history"
array unset excounts
array set excounts {}
for {set replica_id 0} {$replica_id < $num_replicas} {incr replica_id} {
set history_file [open [format $history_filename_format $replica_id $replica_id] "r"]
set allcount 0
set lastnum -1
while {[gets $history_file vals] >= 0} {
incr allcount
if {$lastnum > -1} {
set nownum [lindex $vals 1]
set excounts($nownum.temp) [lindex $vals 2]
if {$nownum != $lastnum} {
set min [expr min($nownum,$lastnum)]
set max [expr max($nownum,$lastnum)]
if {[info exists excounts($min-$max)]} {
set excounts($min-$max) [expr $excounts($min-$max)+1]
} else {
set excounts($min-$max) 1
}
set lastnum $nownum
}
} else {
set lastnum [lindex $vals 1]
}
}
set excounts(allcount) [expr $allcount/2]
}
for {set replica_id 0} {$replica_id < $num_replicas-1} {incr replica_id} {
set partner [expr $replica_id+1]
set temp1 $excounts($replica_id.temp)
set temp2 $excounts($partner.temp)
set excount [expr $excounts($replica_id-$partner)/2]
set pdes [expr (double($excount))/$excounts(allcount)]
puts "EXCHANGE_RATIO ${temp1} ${temp2} ${excount} ${excounts(allcount)} ${pdes}"
}
}
Save the above code top pdes.tcl. Then in console do:
tclsh
source job0.conf
source pdes.tcl
Norman Geist
Von: owner-namd-l_at_ks.uiuc.edu <mailto:owner-namd-l_at_ks.uiuc.edu> [mailto:owner-namd-l_at_ks.uiuc.edu <mailto:owner-namd-l_at_ks.uiuc.edu> ] Im Auftrag von Chitrak Gupta
Gesendet: Montag, 25. Januar 2016 06:16
An: NAMD list < <mailto:namd-l_at_ks.uiuc.edu> namd-l_at_ks.uiuc.edu>
Betreff: namd-l: calculating replica exchange acceptance ratio
Dear all,
I am running replica exchange simulation using NAMD. Normally, the log file contains the exchange acceptance ratios at the end. However, my job ended prematurely (due to exceeding of walltime on the cluster), and the log file does not have the acceptance ratio information at the bottom. Is there a way I could calculate it from the log file entries? Has anyone ever done this?
Best regards,
Chitrak.
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