[gmx-users] choosing box vectors

[gromacs query]

Dear Justin,

Thanks a lot. I used this and it works fine:

editconf -f final.pdb -o final.gro -c -d 0.0

regards,
Jiomm


On Sat, Jun 15, 2013 at 3:09 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 6/14/13 8:08 PM, gromacs query wrote:
>
>> Dear Justin,
>>
>> I saw your tutorial (
>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin/**
>> gmx-tutorials/membrane_**protein/03_solvate.html<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?
>>
>>
> Omit "-bt cubic" from your command and it should work fine.
>
>
> -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>
>