[gmx-users] Periodic Molecules

[Lakshman Ji Verma]

Thanks Justin.

On Tue, May 29, 2018 at 11:09 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>>> <https://maps.google.com/?q=Virginia+Tech+Department+of+Biochemistry&entry=gmail&source=g>
>>>
>>> 303 Engel Hall
>>> 340 West Campus Dr.
>>> Blacksburg, VA 24061
>>>
>>> jalemkul at vt.edu | (540) 231-3129
>>> http://www.thelemkullab.com
>>>
>>> ==================================================
>>>
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-request at gromacs.org.
>>>
>>
> --
> ==================================================
>
> 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
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>