[gmx-users] Fwd: geometry optimization of metalloenzyme

[Justin Lemkul]

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 <jalemkul at 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
>>
>> --
>> ==================================================
>>
>> 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
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==================================================
>>
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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

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================