AW: Turning off and back on fixed atoms

From: Norman Geist (
Date: Fri Oct 28 2016 - 04:40:22 CDT

Are you sure that namd-2.12 allows to re-read the fixedatomsfile?


Von: [] Im Auftrag
von Radak, Brian K
Gesendet: Donnerstag, 27. Oktober 2016 19:05
An:; Norman Geist <>
Betreff: RE: namd-l: Turning off and back on fixed atoms


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
To: <>
Subject: namd-l: Turning off and back on fixed atoms



I'd 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


Best wishes


Norman Geist

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