From: Norman Geist (norman.geist_at_uni-greifswald.de)
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!"
checkpoint
set steps [stepspercycle]
set curr [firsttimestep]
dcdfreq $steps
run $steps
dcdfreq 0
firsttimestep $curr
revert
}
dcdframe_init
run 100
dcdframe
run 100
dcdframe
If anybody else need it.
Norman Geist
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
von Norman Geist
Gesendet: Mittwoch, 9. November 2016 09:06
An: namd-l_at_ks.uiuc.edu; 'Brian Radak' <bradak_at_anl.gov>
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: 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 Brian Radak
Gesendet: Dienstag, 8. November 2016 16:22
An: <mailto:namd-l_at_ks.uiuc.edu> namd-l_at_ks.uiuc.edu; Norman Geist <
<mailto:norman.geist_at_uni-greifswald.de> norman.geist_at_uni-greifswald.de>
Betreff: Re: namd-l: Trigger DCD frame from TCL?
I think the DCD standard expects/requires evenly spaced frames, so, probably
not?
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.
HTH,
Brian
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 brian.radak_at_anl.gov <mailto:brian.radak_at_anl.gov>
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