RE: Turning off and back on fixed atoms

From: Radak, Brian K (
Date: Thu Oct 27 2016 - 12:05:27 CDT

Actually getting NAMD to permit toggling of features is actually not too tough - the question is whether or not the actual forces, etc. are still being correctly computed as a result.

I'm not familiar with Tiger2A, but the obvious concern is in how one properly handles a fluctuating number of degrees of freedom. Is there a proposed solution to this problem? What is the desired behavior for things like the virial?

My guess is that you will have to intermittently read, write, and reload a PDB file specifying the fixed selection and then reallocate the structure from the PSF (using reinitatoms) - this should be possible in 2.12, but it is still a beta feature for sure.

Brian Radak
Postdoctoral Appointee
Leadership Computing Facility
Argonne National Laboratory

9700 South Cass Avenue, Bldg. 240
Argonne, IL 60439-4854
(630) 252-8643
From: [] on behalf of Norman Geist []
Sent: Thursday, October 27, 2016 5:14 AM
Subject: namd-l: Turning off and back on fixed atoms


Id like to implement the Tiger2A REMD via the TCL interface, using the common API replicaSend/Recv etc. This would require to be able to turn on and off fixed atoms and should also allow to change which atoms are fixed, between run commands.

I know this is not possible so far, but I guess people would appreciate this feature.

Best wishes

Norman Geist

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