From: Brian Radak (bradak_at_anl.gov)
Date: Wed Nov 09 2016 - 07:34:48 CST
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.
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
> 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.
> 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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