Re: Targeted MD in NAMD 3.0?

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Wed Oct 14 2020 - 08:48:39 CDT

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.

Best,
Jerome

----- On 13 Oct 20, at 18:18, Smith, Harper E. 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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