VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun Mar 13 2011 - 11:49:26 CDT

On Sun, Mar 13, 2011 at 11:14 AM, leila karami <karami.leila1_at_gmail.com> wrote:
> Hello,
>
> I want to save trajectory file as *.trr from HISTORY file that has box
> vectors in triclinic box in every frame as the following in angstrom
> unit:
>
>  34.60       0 0.00       00.00
>
>  17.30        29.97       00.00
> 0 0.00     00.00       100.00
>
> I went to the VMD 1.8.7 console and typed “package require pbctools ,
> it printed 2.5 then I typed commands in VMD console (or TK console) to
> set pbc as the following:
>
> pbc set {{34.60 0.000 0.00} {17.30 29.97 0.00} {0.00 0.00 100.0}} -all –namd
>
> but i obtained bellow vectors that are not correct.
>
> box[ 0]={ 3.46000e+00, 0.00000e+00, 0.00000e+00}
>
> box[ 1]={ 2.11886e-16, 3.46048e+00, 0.00000e+00}
>
> box[ 2]={ 6.12303e-16, 3.53546e-16, 1.00000e+01}
>
> also, I typed:
>
> pbc set {34.6 34.6 100. 90. 90. 60.} -all -vmd
>
> That correspond with {a b c alpha beta gamma} that alpha beta gamma
> are angles between b and c, a and c, a and b, respectively.
>
> But it couldn’t get me correct answer in *.trr as the following:
>
> 3.460       0.000       00.00
>  1.730        2.997       00.00
>  0.000       0.000       10.00
>
> Would anyone help me to get correct box vectors in *.trr?

what is wrong about the last one?

axel.

>
>
>
>
> Thanks in advance
>
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.