Re: REMD and sortreplicas program

From: Horia Jalily Hasani (
Date: Thu Sep 08 2016 - 12:22:39 CDT

Hi Norman,

Thanks for your reply.
Yes, it's normal parallel tempering.
I currently do an exchange after 50,000 steps, and so I get an entry in the
history file only every 50,000 steps. Based on what you mentioned, this
could explain the reason for sortreplicas giving me lesser frames in the
sorted dcd files. I have only 50 entries and so I get only 50 frames in the
sort.dcd file, whereas the initial dcd file has 2000 frames.

So I will need to increase the entries in the history file to for example
every 1000 steps instead of doing it based on steps_per_run parameter. And
for that I suppose I will need to modify this section of the replica.namd

while {$i_run < $num_runs} {

  run $steps_per_run
  incr i_step $steps_per_run
  set TEMP $saved_array(TEMP)
  set POTENTIAL [expr $saved_array(TOTAL) - $saved_array(KINETIC)]
  puts $history_file "$i_step $replica(index) $NEWTEMP $TEMP $POTENTIAL"

  if { $i_run % 2 == 0 } {
    set swap a; set other b
  } else {
    set swap b; set other a

Please advise if I am on the right track and what would be the best way to
edit it.


On Thu, Sep 8, 2016 at 12:41 AM, Norman Geist <> wrote:

> What kind of REMD did you perform? Just normal parallel tempering? If so,
> you should get all the frames in the sorted dcds for which you also have
> the corresponding history entry. Also, how did you call sortreplicas?
> Norman Geist
> *Von:* [] *Im
> Auftrag von *Horia Jalily Hasani
> *Gesendet:* Donnerstag, 8. September 2016 02:11
> *An:* <> <>
> *Betreff:* namd-l: REMD and sortreplicas program
> Hi,
> I have been performing REMD and I wonder if someone could give me a hint
> in the analysis part. When it comes to using the sortreplicas for sorting
> the dcd files and history files based on temperature, the program seems to
> take "only frames with the biasing potential V (d, i)" (quoted from
> the One-dimensional REUS tutorial).
> For example, if I give it trajectories each of which have 2000 frames, I
> end up getting only 50 frames in the sorted dcd files. But I am interested
> in having all the 2000 frames sorted based on temperature without
> considering the potential at that point.
> I would appreciate if anyone could give me a hint related to
> the sortreplicas program and if there is an alternative way of sorting the
> outputs based on temperature.
> Thanks,
> Horia

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