VMD-L Mailing List

From: leila karami (karami.leila1_at_gmail.com)
Date: Sun Mar 13 2011 - 10:14:49 CDT

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?

Thanks in advance