VMD-L Mailing List

From: leila karami (karami.leila1_at_gmail.com)
Date: Sat Apr 09 2011 - 08:44:04 CDT

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