Hi Justin, "A cubic box is already as compact as it can be." That's true and I understand that :) it's just that I have faced similar issues with trjconv that Mala appears to be grappling with, and this combination has always resolves it for me. I don't know why. I can attach test files that show this behavior.
Rajat On Fri, 8 Feb 2019, 5:27 pm Justin Lemkul <jalem...@vt.edu wrote: > > > On 2/8/19 5:17 AM, Rajat Desikan wrote: > > Hi Mala, > > Please combine -center with "-pbc mol -ur compact" and check. > > Compact unit cell representation is only useful for dodecahedral and > octahedral boxes. A cubic box is already as compact as it can be. > > -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 > > jalem...@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-requ...@gromacs.org. > -- 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-requ...@gromacs.org.