VMD-L Mailing List
From: leila karami (karami.leila1_at_gmail.com)
Date: Sat Apr 09 2011 - 08:44:04 CDT
- Next message: Axel Kohlmeyer: "Re: box vectores in .trr"
- Previous message: John Stone: "Re: electrostatic potential maps."
- Next in thread: Axel Kohlmeyer: "Re: box vectores in .trr"
- Reply: Axel Kohlmeyer: "Re: box vectores in .trr"
- Reply: Matt Watkins: "Re: box vectores in .trr"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
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
- Next message: Axel Kohlmeyer: "Re: box vectores in .trr"
- Previous message: John Stone: "Re: electrostatic potential maps."
- Next in thread: Axel Kohlmeyer: "Re: box vectores in .trr"
- Reply: Axel Kohlmeyer: "Re: box vectores in .trr"
- Reply: Matt Watkins: "Re: box vectores in .trr"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]