[gmx-users] Box generation for monoclinic crystal - regd

[Mark Abraham]

On 11/04/2012 4:13 AM, ramesh cheerla wrote:
> Dear Mark,
>
>              Thank you for reply, sorry for not being very clear, 
> Here  my doubt is can i use  triclinic box for the simulations of the 
> crystal whose unit cell is monoclinic. As i said earlier  i have tried 
> editconf as
> editconf -f input.gro -o out_box1.gro  -bt triclinic -box 3.22 2.608 
> 7.792  -angles 90  125.4 90
> it gave the following warning
>
> WARNING: Triclinic box is too skewed.
>
> for clarity here i am sending a part of the output file generated by 
> the editconf
> God Rules Over Mankind, Animals, Cosmos and Such
>  6528
>     1PEGA    C1    1  -0.025   0.408  -0.045
>     1PEGA    C2    2  -0.015   0.326   0.084
>      ::::::::::::::::::::::::::::::::::::::::::::::::::::::::;
>      3.22000   2.60800   6.35148   0.00000   0.00000   0.00000   
> 0.00000  -4.51376  -0.00000
> if i change the angles while using the editconf i observed the 
> following changes
>
> editconf -f input.gro -o out_box2.gro  -bt triclinic -box 3.22 2.608 
> 7.792  -angles 90  90 125.4

Isn't that a totally different box? See editconf -h about -angles.

Mark

> in this case editconf haven't given any warning and the output as follows
>
>  God Rules Over Mankind, Animals, Cosmos and Such
>  6528
>     1PEGA    C1    1   1.477   0.167   0.675
>     1PEGA    C2    2   1.487   0.085   0.804
>      ::::::::::::::::::::::::::::::::::::::::::::::::::::::::;
>    3.22000   2.12585   7.79200   0.00000   0.00000  -1.51077   
> 0.00000  -0.00000  -0.00000
>
> Can you please help me in this regard.
>
> thank you in advance.
>
>
>
>
>
>
>
>
> On Mon, Ap;r 9, 2012 at 11:55 AM, Mark Abraham 
> <Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>> wrote:
>
>     On 9/04/2012 3:22 PM, ramesh cheerla wrote:
>
>         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 for generation of
>         box for the monoclinic crystal, though the crystal is of
>         monoclinic  i am using box type as triclinic
>         i haven't found any specific method for the generation of box
>         for the monoclinic crystal.
>         2) Is there any specific method to generate the box for the
>         monoclinic crystals.
>         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.
>
>
>     This means equation 3.3 of the manual is not true. Maybe beta
>     should be acute? I've no idea of necessity or convention here.
>
>     Inspecting the whole output of editconf is probably instructive,
>     but you've kept all that information to yourself instead of
>     re-thinking how your repeat post might be constructed so as to
>     make it easier / more likely for people help you. Likewise the
>     final line of out_box.gro. Make sure you have read and understood
>     what documentation is available with editconf -h and in manual
>     section 3.2.
>
>     Mark
>     -- 
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