From: Josh Vermaas (joshua.vermaas_at_gmail.com)
Date: Wed Oct 14 2020 - 09:28:14 CDT
I think the current state of the public 3.0 alphas is that colvars and
CUDASOAIntegrate are mutually exclusive. If you turn off
CUDASOAIntegrate, as it stands now you'd go down the old 2.14 codepath
more or less, so the performance will not be all that great.
On 10/14/20 8:15 AM, Giacomo Fiorin wrote:
> Using Colvars instead of the much older TMD implementation makes sense
> in general, but I'm not 100% sure here.
> Enabling Colvars in NAMD 3 on even a few atoms would probably damage
> performance, because of the latency associated with the transmission
> of data between GPU and CPU. On the positive side, it should be easy
> to test if (1) it works and (2) performance is still acceptable on a
> short benchmark.
> FYI it looks like the OpenMM folks have struggled with a similar
> problem and eventually implemented several collective variables
> directly as internal objects, instead of using PLUMED as they had done
> On Wed, Oct 14, 2020 at 9:50 AM Jérôme Hénin <jerome.henin_at_ibpc.fr
> <mailto:jerome.henin_at_ibpc.fr>> wrote:
> Hi Harper,
> I don't know if the NAMD implementation of TMD is supposed to be
> supported in NAMD 3 and beyond, but you can always perform TMD
> using the Collective Variables (Colvars) Module, with a moving
> restraint on a RMSD coordinate.
> ----- On 13 Oct 20, at 18:18, Smith, Harper E.
> <mailto:smith.12510_at_buckeyemail.osu.edu> wrote:
> > Hi mailing list,
> > I want to use NAMD 3.0 alpha 6 with CUDASOAintegrate on to run a
> targeted MD
> > simulation. Although I see TMD output in NAMD 2.12, I do not see
> it after
> > switching.
> > I get several lines that it is active:
> > Info: TMD ACTIVE BETWEEN STEPS 0 and 1250000
> > Info: TMD K 200
> > Info: TMD FILE trimer-post-targeting.tmd
> > Info: TMD OUTPUT FREQUENCY 1000
> > Info: TMD TARGET RMSD AT FIRST STEP -1
> > Info: TMD TARGET RMSD AT FINAL STEP 0
> > .but the relevant output is missing. Is TMD supported in NAMD 3.0?
> > Best,
> > Harper Smith
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