Re: colvars and parallel-tempering with namd2.10

From: Francesco Pietra (
Date: Mon Aug 19 2013 - 01:46:36 CDT

(2) The number of processes is 17 x 9 x 13 = 1989, i.e., correctly LESS
that the number of processors (1024) should be read

(2) The number of processes is 17 x 9 x 13 = 1989, i.e., correctly LARGER
that the number of processors (1024).

sorry fp

On Mon, Aug 19, 2013 at 8:41 AM, Francesco Pietra <>wrote:

> Giacomo: Thanks a lot. The correct layout of harmonic bias improves the
> performance by a very slight margin (1.57 vs previous 1.60 days/ns).
> Anyway, the log file warns about the incorrect layout I used before.
> The wallclock/cpuTime is in huge disagreement, as it indicates a slowdown
> by only two on using these colvars, but it is told in namd performance wiki
> that wallclock is unreliable in looking at performance.
> As to the settings in namd conf file, I can't claim that they are optimal,
> especially for the MPI/OpenMP standard compilation with threads of namd2.9
> on Bluegene (I have another one without threads but I use it for parallel
> tempering)..
> As to the settings:
> (1) One striking - surely well known - observation is that Bluegene
> changes my "margin 0" to "margin 0.48" because it deals of a const pressure
> simulation. Somewhat that contrasts with the indication on the said namd
> wiki.
> (2) The number of processes is 17 x 9 x 13 = 1989, i.e., correctly less
> that the number of processors (1024).
> But there are so many other possibilities of tuning...
> At any event, it seems to me that the only hope is in what you suggested:
> tclBP. Hopefully a script skeleton will be provided by some king namd user
> as I found no similar scripting looking around. Applying so many patches
> might seem to be crazy but I think I have good reasons to do that. Another
> possibility could be to carry out parallel tempering on a system consisting
> of only the parts of the protein that I would like to submit to a thermal
> cycle. However, I have no idea how to recombine this part with the one from
> which it was separated. With the further complication that there is a
> double layer membrane.
> francesco
> On Sun, Aug 18, 2013 at 5:40 PM, Giacomo Fiorin <>wrote:
>> Francesco, the syntax of the "harmonic" bias is not correct. colvars and
>> centers should both be lists, appearing only once in the block.
>> Giacomo
>> On Sat, Aug 17, 2013 at 12:51 PM, Francesco Pietra <
>> > wrote:
>>> >In my opinion you could give the tclBC option a try.
>>> My hope is on this suggestion by Giacomo Fiorin. Unless I did mistakes,
>>> ordinary rmsd colvars turns out to slow down the simulation beyond
>>> feasibility with my system of 500,000 atoms (protein, peptide ligands, POPC
>>> bilayer, TIP3 water).
>>> I set rmsd colvars for about 1300 CA atoms in six different segments
>>> (protein-ligands mostly well defined by Xray diffr and well behaving in
>>> namd2.9 equilibration charmm ff), leaving out only those poorly defined--001a11c33676450e6904e4474dc9--

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