From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Thu Nov 10 2016 - 02:09:22 CST
Thanks guys, for now it seems I can get an approximation of what I need with
the following workaround. Even though it's not beautiful, it works for now
=)
I'm looking forward for NAMD getting such a command in the future, aswell as
the fixedatoms turn on/off stuff.
Best wishes
Norman Geist
[… usual namd setup …]
#make sure dcdfreq was != 0 before calling this
proc dcdframe_init {} {
puts "Initializing on-demand coords!"
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
> -----Ursprüngliche Nachricht-----
> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> Auftrag von Jim Phillips
> Gesendet: Mittwoch, 9. November 2016 23:48
> An: namd-l_at_ks.uiuc.edu; Brian Radak <bradak_at_anl.gov>
> Cc: Norman Geist <norman.geist_at_uni-greifswald.de>
> Betreff: Re: AW: namd-l: Trigger DCD frame from TCL?
>
>
> The rule NAMD uses is that a DCD frame is written when the corresponding
> timestep is first reached. This avoids re-writing the initial state or
> repeating frames when "run 0" is called. An explicit command to append a
> frame to a DCD file would be useful.
>
> Jim
>
> On Wed, 9 Nov 2016, Brian Radak wrote:
>
> > Ah yes, so this is a problem that I understand - I just gave the REMD
> > developers the benefit of the doubt that they had this working as well.
> When
> > I implemented simulated tempering, the solution was to invert the cycle
so
> > that the exchange is attempted first and then MD is run. This ensures
that
> > the final frame (which must be a multiple of DCDFreq) is drawn with the
> > reported Hamiltonian parameters.
> >
> > HTH,
> >
> > Brian
> >
> >
> > On 11/09/2016 02:05 AM, Norman Geist wrote:
> >>
> >> 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]
> *Im
> >> Auftrag von *Brian Radak
> >> *Gesendet:* Dienstag, 8. November 2016 16:22
> >> *An:* namd-l_at_ks.uiuc.edu; Norman Geist <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>
> >>
> >
> > --
> > 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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