[gmx-users] Info regarding restrained minimization, equilibration & production

[Justin Lemkul]

On 5/7/20 8:47 AM, Paolo Costa wrote:
> Dear Justin,
>
> I thought too.
> In case, could you please indicate me how I can constrain the interatomic
> distance of a desired molecule, in such case the POM molecule?

Define [constraints] in the topology for all relevant interatomic distances.

-Justin

> Thanks a lot.
>
> Paolo
>
> Il giorno gio 7 mag 2020 alle ore 14:44 Justin Lemkul <jalemkul at vt.edu> ha
> scritto:
>
>>
>> On 5/7/20 8:41 AM, Paolo Costa wrote:
>>> Dear Justin,
>>>
>>> thanks a lot for your valuable information.
>>> The system (Keggin anion, POM) I am trying to simulate is almost
>> identical
>>> to the one already studied in literature (doi: 10.1021/jp077098p).
>>> In the SI of this work, the authors stated "*Keggin anions are treated as
>>> rigid particles thus keeping constant the distances between the different
>>> metal and oxygen atom".*
>>> That means they did not parametrize the bonded interactions for such
>>> molecule, isn't?
>> That sounds to me like all interatomic distances were fixed via
>> constraints, but you should contact the corresponding author to be sure,
>> and ask for example inputs.
>>
>> -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

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