[gmx-users] choosing box vectors

[gromacs query]

Dear Justin,

I saw your tutorial (
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html
)

But my case is different. I can not even generate tpr file (trjconv as
tutorial says) as it need box info

Can you please suggest what can be the best possible way? If I just use
system size dimension (X, Y Z) and do mimization it break my system in
parts!


How to choose optimum box vector in such case?

regards,



On Sat, Jun 15, 2013 at 2:49 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 6/14/13 7:37 PM, gromacs query wrote:
>
>> 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?
>>
>>
> You're specifying a cubic box, but for most membrane systems, that's
> probably wrong.  What editconf is doing is determining what box vectors are
> necessary, then since you're telling it to make the box cubic, it's forcing
> all of the vectors to be the same.  Apparently you have at least one
> dimension that, in this case, is 14.737 nm in length, and then all other
> vectors are then set to the same value.
>
> -Justin
>
>
> --
> ==============================**==========
>
> 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>
>
> ==============================**==========
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>