AW: Trigger DCD frame from TCL?

From: Norman Geist (
Date: Wed Nov 09 2016 - 02:48:33 CST

Seems I can get an approximation of what I need using the following hacks:


  [. usual namd setup .]


  #make sure dcdfreq was != 0 before calling this

  proc dcdframe_init {} {

    puts "Initializing individualized DCD frame generation!"

    run 0

    dcdfreq 0



  proc dcdframe {} {

    puts "Trigger DCD frame!"


    set steps [stepspercycle]

    set curr [firsttimestep]

    dcdfreq $steps

    run $steps

    dcdfreq 0

    firsttimestep $curr





  run 100


  run 100



If anybody else need it.


Norman Geist


Von: [] Im Auftrag
von Norman Geist
Gesendet: Mittwoch, 9. November 2016 09:06
An:; 'Brian Radak' <>
Betreff: AW: namd-l: Trigger DCD frame from TCL?


Thanks Brian,


I know about the "output" command but wanted to avoid using 1. Many thousand
files and 2. Using external tools from within namd (random segfault issue
with REMD and GPUs). Looks I will have to postprocess my trajectories to
extract the desired frames afterwards. But anyway the REMD algorithms should
actually output frames after exchange attempts, not before as it currently
is, this is hard to do with namd and dcdfreq and is somewhat wrong. This is
because an accepted replica by the metropolis criterion should contribute
its current state to the accepted temperature, not the one it was coming
from. Depending on the length of one run, the sampling error can be very
high, which can result in non-boltzmann statistics at the respective
temperature trajectories.


Since there are so many TCL commands related to multicopy algorithms, there
is likely an interest in having such a "dcdframe" command aswell.


Norman Geist


Von: <>
[] Im Auftrag von Brian Radak
Gesendet: Dienstag, 8. November 2016 16:22
An: <>; Norman Geist <
Betreff: Re: namd-l: Trigger DCD frame from TCL?


I think the DCD standard expects/requires evenly spaced frames, so, probably

A close alternative is the "output <basename>" command, which triggers a
writing of coordinates, velocities, and extended system files based on the
provided basename. It's not pretty, but you can paste together a bunch of
binCoordinate files with catdcd when you are done.




On 11/08/2016 09:12 AM, Norman Geist wrote:

Hey there,


is there any TCL command that can be used to trigger a DCD frame, without
using dcdfreq?


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

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