On 4/9/20 4:25 PM, Nadia Elghobashi-Meinhardt wrote:
Thank you, Justin.
I am still struggling with constraints.
I am trying to use "freezegrps" and "freezedim"
to run an NVT equilibration.
However, when I try to build the binary using my optimized structure, I get
either "Segmentation fault" or the following error:
"free(): invalid next size (fast)
Aborted"
What do these messages indicate? Problem in memory allocation?
All of this is probably a downstream effect of a simulation that is
unstable and crashed.
Freezing is totally artificial and I strongly discourage using it. The
crash may be due to failure to use energygrp_exclusions when freezing or
due to intrinsic instability of the system that even freezing cannot
overcome.
-Justin
On Thu, Apr 2, 2020 at 9:26 PM Justin Lemkul <jalem...@vt.edu> wrote:
On 4/2/20 3:23 PM, Nadia Elghobashi-Meinhardt wrote:
Hello everyone,
I am trying to minimize the potential energy of a
metalloenzyme containing Ni and Fe atoms.
What is the best way to constrain (fix?) the position of the active site
atoms
during the geometry optimization?
I have tried introducing bonds with relatively high force constants and
alternatively, tried introducing a [constraints] section,
but the atoms are still not staying put.
Bonds or constraints will maintain distances between atoms (relative
position) but not absolute position.
Or should one use extra position restraints?
If the absolute position matters, yes. I would think the approach of
adding restraints or constraints between atoms would be more meaningful
given that preserving coordination geometry is often the defect in MM
treatment of transition metals.
-Justin
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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
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