VMD-L Mailing List

From: Matt Watkins (mattwatkinsuk_at_gmail.com)
Date: Sat Apr 09 2011 - 17:47:06 CDT

Hi,

Could be the same problem I experienced a while ago. In my particular
case I could fix it with the small change to the plugin code here

http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/14581.html

Matt

p.s. sorry axel for previous reply to you not the list,

On Sat, Apr 9, 2011 at 2:44 PM, leila karami <karami.leila1_at_gmail.com> wrote:
> Hello,
>
>
> I have history file (one of outputs of DL_POLY software) with box vectors
> (angstrom) in triclinic box as following:
>
>  34.60       0.000       0.000
>  17.30        29.97       0.000
>  0.000       0.000       100.0
>
> I want to convert HISTORY file to .trr trajectory file with VMD program.
>
> I used vmd 1.8.7 to convert and typed in the VMD console:
> package require pbctools
> it printed: 2.5
>
>  and then I 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
>
> And another pbc sets,for example; pbc set {3.4  3.4  10.0  90.  90.  60.}
> that correspond to {a b c alpha beta gama} –namd –all  or pbc set {3.4  3.4
> 10.0  {90.  90.  60.}}. But I couldn’t obtain the box vectors correctly in
> .trr trajectory file.
>
> The values in *.trr are in nano meter.
>
> For example I got these values with changing pbc sets in vmd console in .trr
> trajectory files:
>
>      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}
>
> Or
>
>      box[    0]={ 3.46000e+00,  0.00000e+00,  0.00000e+00}
>
>      box[    1]={ 1.73000e+00,  2.99645e+00,  0.00000e+00}
>
>      box[    2]={ 6.12303e-16,  5.00000e+00,  8.66025e+00}
>
> in fact I must obtain box vectors as following in .trr trajectory file:
>
>      box[    0]={ 3.46000e+00,  0.00000e+00,  0.00000e+00}
>
>      box[    1]={ 1.73000e+00,  2.99645e+00,  0.00000e+00}
>
>      box[    3]={ 0.00000e+00,  0.00000e+00,  1.00000e+01}
>
>
>
> Would anyone please help me to obtain box vector correctly in .trr
> trajectory file?
>
>  Thanks in Advance,
>
> --
>
> Leila Karami
> Ph.D. student of Physical Chemistry
> K.N. Toosi University of Technology
> Theoretical Physical Chemistry Group
>