[gmx-users] Monoclinic crystal simulations- gromacs - Regd

ramesh cheerla rameshgromacs at gmail.com
Sat Apr 7 07:14:02 CEST 2012

Dear Gromacs users,

                           I am planing to simulate a polymeric crystal in
gromacs, which is of monoclinic unit cell with cell parameters a = 0.805 nm
b = 1.304 nm and c = 1.948 nm and beta = 125.4 deg. my crystal is of 424
type  i.e 4 unit cells along 'a' direction  '2' unit cells along 'b'
direction and 4 unit cells along 'c' direction.
So my box vector lengths are a = 3.22 nm, b = 2.608 nm, c = 7.792 nm.
I  am using editconf to generate box for this crystal as:

editconf -f input.gro -o out_box.gro  -bt tric -box 3.22 2.608 7.792
-angles 90  125.4 90

Here i have some doubts:

1) Am i using the editconf in correct manner by mentioning box type  as
triclinic though the crystal is of monoclinic
2) Is there any specific method to generate the box for the monoclinic
3) The notations for the lattice parameters of the crystal i.e 'a' , 'b' ,
'c' and angles alpha, beta , gamma used by crystallography and the gromacs
editconf are the same or different, why because if i use editconf as above
i am getting the following warning:

WARNING: Triclinic box is too skewed.

Thank you in advance,

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