[gmx-users] Scale Triclinic Box

[Justin Lemkul]

On 4/4/20 5:07 PM, Maryam Sadeghi wrote:
> 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?

You can apply a scaling vector with editconf -scale as I suggested in my 
last message, but I do not think it will do what you want. That's the 
only GROMACS tool that has any such capability, so if that doesn't work, 
GROMACS isn't going to do what you want.

-Justin

> 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 <jalemkul at 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
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==================================================
>>
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-- 
==================================================

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

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================