Hi Salman, Tnx for the info, I actually want to do the cold-compression on my crystalline structure. So basically I need to both compress and expand the a and b parameters of the unit cell (the c parameter is already optimized)... so it's not just building a supercell, but rather scaling only 2 parameters of the unit cell simultaneously while remaping the new coordinates inside the scaled cell... could "gmx genconf -nbox ... ... ..." handle this?
Best Maryam On Fri, Apr 3, 2020, 2:54 PM Salman Zarrini <salman.zarr...@gmail.com> wrote: > Hi Maryam, > > The ``gmx genconf -nbox 2 2 1'' is your friend to generate a supercell, I > am just not sure if it could handle a triclinic cell. > Since your unit cell is not that large, you even can use Avogadro or > ASE-gui which both are good molecule editors and visualizers. > > Cheers, > Salman > > On Fri, Apr 3, 2020 at 3:55 PM Maryam Sadeghi <maryam.sadeghi...@gmail.com > > > wrote: > > > Dear All, > > > > I need to scale the a and b parameters of a triclinic crystalline unit > > cell. When I use the editconf command, only the cell parameters are > scaled > > while the coordinates of atoms are not remapped in the new cell. > > > > gmx editconf -f CONTCAR.pdb -o scl0.2.pdb -bt triclinic -box 0.3560 > 0.5686 > > 1.9724 -angles 90.00 126.91 90.00 > > > > The unit cell consists of 4 polymer chains, each chain having 7 repeating > > (C-O-C) units. The system has 3 atom types (C, H, O), 196 atoms, 192 > bonds, > > 340 angles and 376 dihedrals. > > > > The original cell parameters are: > > a: 0.79620 nm, b: 1.27140 nm, c: 1.9724 nm, alpha: 90.00, beta: 126.91, > > gamma: 90.00 > > > > Any suggestions how I can remap the coordinates (keeping the bonds and > > angles constant) together with scaling the box? > > > > Thanks, > > -- > > 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. > -- 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.