VMD-L Mailing List

From: Olaf Lenz (olenz_at_icp.uni-stuttgart.de)
Date: Thu Mar 10 2011 - 07:07:35 CST

Hello!

On 03/10/2011 01:11 PM, leila karami wrote:
> I want to gain *.trr file from *.xyz or HISTORY file with VMD 1.8.7
> program. simulated box is triclinic with box vectors:
> 3.460 0.000 0.000
> 1.730 2.997 0.000
> 0.000 0.000 10.00
>
> but in *.trr zero box vectors are reported as the following:
> box (3x3):
> box[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> box[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> box[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
>
> Could anyone please advice me how to solve this?how to fix triclinic box
> with VMD or other alternative?

The .xyz-format does not store the box vectors at all, therefore it is
not surprising that they are not set when you save a .trr file.
What you can do is to load the .xyz file first, and then set the box
vectors via the pbctools, like

  pbc set {{3.460 0.000 0.000} {1.730 2.997 0.000} {0.000 0.000 10.00}}
-namd -all

(Type this command into the VMD console).

Cheers
   Olaf 

-- 
Dr. rer. nat. Olaf Lenz
Institut für Computerphysik, Pfaffenwaldring 27, D-70569 Stuttgart
Phone: +49-711-685-63607