[gmx-users] gmx traj output

Mohsen Ramezanpour ramezanpour.mohsen at gmail.com
Wed Apr 25 18:01:06 CEST 2018


Thanks, Justin.

Cheers,
Mohsen

On Tue, Apr 24, 2018 at 7:09 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 4/23/18 11:08 PM, Mohsen Ramezanpour wrote:
>
>> Hi Gromacs users,
>>
>> I am using gmx traj to get the box size (X, Y, Z).
>> I use the following command:
>>
>> echo 0 | gmx traj  -f trajectory.xtc  -s md.tpr  -ob box.xvg  -xvg none
>>
>> The output has 77 columns.
>> 1st is the time step,
>>
>> 2nd, 3rd, and 4th seem to be the X, Y, and Z size of the box.
>> I was wondering what are the 5th, 6th, and 7th columns giving, exactly?
>>
>
> The output is the half-matrix of the box tensor. The first three elements
> are the diagonal, the remaining three are the off-diagonal elements.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>



-- 
*Rewards work better than punishment ...*


More information about the gromacs.org_gmx-users mailing list