[gmx-users] Periodic Molecules
jalemkul at vt.edu
Tue May 29 18:09:42 CEST 2018
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.
> 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
>>> 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 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
>> Gromacs Users mailing list
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> * 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.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
More information about the gromacs.org_gmx-users