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

[ramesh cheerla]

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
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>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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