Hi Justin, I actually want to scale the box (both moving the chains apart and close to each other by changing the a and b parameters of the cell). I don't want to run any dynamics at this point as I have already done quantum mechanics minimization on this structure. When I use the editconf command the cell parameters change but the coordinates of the atoms remain unchanged, i.e. by compression the polymer chains remain outside of the cell... I was wondering if editconf could scale the coordinates proportionally with the cell parameters without distorting the bonds lengths?
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 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 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. Best Maryam On Sat, Apr 4, 2020, 4:54 AM Justin Lemkul <jalem...@vt.edu> wrote: > > > On 4/3/20 11:16 PM, Maryam Sadeghi wrote: > > 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? > > It sounds like you need to actually perform a simulation in which high > pressure is applied to compress the box. genconf is for duplicating a > box N times in each dimension, and while you can change box vectors and > scale coordinates with editconf (-scale option), this is not the same as > compressing them and bond lengths, etc. will become distorted. > > -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.