[gmx-users] Periodic Molecules

[Justin Lemkul]

On 5/29/18 12:04 PM, Lakshman Ji Verma wrote:
> Thanks Justin. A follow up question for my better understanding.
>
> Does it mean that with “periodic-molecules” False, the periodic images
> won’t affect interactions in the actual simulation box, whereas they will
> affect if I keep “periodic-molecules” True?

No. Again, normal PBC and "periodic molecules" are different concepts.

-Justin

> Thanks
> Lakshman
>
> On Tue, May 29, 2018 at 10:53 AM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> On 5/29/18 11:50 AM, Lakshman Ji Verma wrote:
>>> What difference it will make I keep Periodic molecules option True or
>> False?
>>> I read the manual but couldn’t understand more than keeping it False will
>>> be faster.
>> The "periodic-molecules" option is for use with "infinite" systems like
>> CNT, surfaces, etc. That is, the topology specifies bonds that always
>> span a periodic boundary. This option is distinct from normal PBC.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 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
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

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

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