[gmx-users] choosing box vectors

[gromacs query]

Dear Justin,

Thanks for reply. Yes sorry indeed its taking box vector from pdb (which I
dont want to use as I think they are wrong). In my case if I have already
water molecules in my system then if I use:

editconf -f del.pdb -o del.gro -c -d 0.0 -bt cubic

even now also I see pbc box (in vmd) its quite big than system as you can
see from output

    system size : 10.707 11.077  7.493 (nm)
    diameter    : 14.737               (nm)
    center      :  6.928  6.932  6.936 (nm)
    box vectors :  0.000  0.000  0.000 (nm)
    box angles  :   0.00   0.00   0.00 (degrees)
    box volume  :   0.00               (nm^3)
    shift       :  0.441  0.436  0.432 (nm)
new center      :  7.369  7.369  7.369 (nm)
new box vectors : 14.737 14.737 14.737 (nm)
new box angles  :  90.00  90.00  90.00 (degrees)
new box volume  :3200.60               (nm^3)


What should I do?

regards,



On Sat, Jun 15, 2013 at 1:37 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 6/14/13 4:58 PM, gromacs query wrote:
>
>> Dear All,
>>
>> I have two different membrane systems (membrane with waters only) already
>> with me. So I dont need to add solvent molecules.
>>
>> So to start with simulation I need box size (last line in gro file). I
>> used
>> following command (for both cases):
>>
>> editconf -f del.pdb -o del.gro -c -bt cubic
>>
>>
>> First case details:
>>
>>      system size : 10.707 11.077  7.493 (nm)
>>      diameter    : 14.737               (nm)
>>      center      :  6.928  6.932  6.936 (nm)
>>      box vectors : 10.707 11.077  7.493 (nm)
>>      box angles  :  90.00  90.00  90.00 (degrees)
>>      box volume  : 888.68               (nm^3)
>>      shift       : -1.574 -1.394 -3.190 (nm)
>> new center      :  5.353  5.538  3.747 (nm)
>>
>>
> I don't see how this is possible.  You used -bt cubic, but you clearly (1)
> don't want that, because the system is rectangular and (2) a cubic box is
> not produced.  Why even use editconf?  Clearly the input .pdb file has
> correct box vectors in it already and does not require any modification.
>
>
>
>>
>> Second case details:
>>
>>      system size : 10.065 11.826  9.911 (nm)
>>      diameter    : 16.459               (nm)
>>      center      :  9.229  9.229  9.229 (nm)
>>      box vectors : 18.459 18.459 18.459 (nm)
>>      box angles  :  90.00  90.00  90.00 (degrees)
>>      box volume  :6289.31               (nm^3)
>>      shift       :  0.000  0.000  0.001 (nm)
>> new center      :  9.229  9.229  9.229 (nm)
>>
>>
> Here, there are probably erroneously large vectors written in the .pdb
> file already.
>
> -Justin
>
>
>
>>
>> As I have solvents already so my box size as a rule should be (Maximum X -
>> Minimum X), (Maximum Y - Minimum Y), (Maximum Z - Minimum Z). This indeed
>> I
>> found to be correct for my first case in which box dimensions in gro file
>> =
>> 10.707 11.077  7.493
>>
>> But why in my second case box dimension in gro file = 18.459 18.459
>> 18.459.
>> Surprisingly its is equal to Maximum X + Minimum X of my system and all
>> are
>> same being 18.459. Rather it should be (Maximum X - Minimum X), (Maximum Y
>> - Minimum Y), (Maximum Z - Minimum Z) as in first case.
>>
>> Also in VMD I saw gro files. In first case pbc box completely fits the
>> membrane water system but in second case pbc box is un-necessarily large
>> as
>> it is using 18.459 18.459 18.459
>>
>>
>> I am confused why in second case it chose Maximum X + Minimum X unlike in
>> first case?
>>
>> please suggest,
>>
>> thanks,
>> Jiom
>>
>>
> --
> ==============================**==========
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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