From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Fri Oct 28 2016 - 04:40:22 CDT
Are you sure that namd-2.12 allows to re-read the fixedatomsfile?
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
von Radak, Brian K
Gesendet: Donnerstag, 27. Oktober 2016 19:05
An: namd-l_at_ks.uiuc.edu; Norman Geist <norman.geist_at_uni-greifswald.de>
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.
Leadership Computing Facility
Argonne National Laboratory
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Argonne, IL 60439-4854
From: <mailto:owner-namd-l_at_ks.uiuc.edu> owner-namd-l_at_ks.uiuc.edu
[owner-namd-l_at_ks.uiuc.edu] on behalf of Norman Geist
Sent: Thursday, October 27, 2016 5:14 AM
To: <mailto:namd-l_at_ks.uiuc.edu> namd-l_at_ks.uiuc.edu
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
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