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

[Tsjerk Wassenaar]

Hi Ramesh,

Maybe it is easier, and less error-prone, to work in PDB format,
specifying the box as a CRYST1 record. You can use the PDB format
anywhere in your workflow where GRO format is used.

Cheers,

Tsjerk


On Tue, Apr 10, 2012 at 8:13 PM, ramesh cheerla <rameshgromacs at gmail.com> 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
> 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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>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands