[gmx-users] last line in .gro file
Vishal Agarwal
vishal.iitian at gmail.com
Wed Feb 3 03:44:20 CET 2010
Hi Tsjerk,
Thanks for replying. I was going through the pdb format dcoument on the PDB
webpage. I found that the box corresponds to the following:
a b(cos(gama)) c(cos(beta))
0 b(sin(gama)) c(cos(alpha) - cos(beta) cos(gama) / sin(gama)
0 0 V/(ab sin(gama))
where V = abc(1 - (cos(alpha))^2 - (cos(beta))^2 - (cos(gama))^2+
2cos(alpha) cos(beta) cos(gama))^1/2
This corresponds to general form in representing these vectors. The
following code also desolves to this form.
Thank you again.
Best,
Vishal
P.S. I thank all who have replied to this mail.
On Tue, Feb 2, 2010 at 3:44 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> Hi Vishal,
>
> Here is a python function that generates a triclinic representation
> given a definition with lengths and angles. The argument L is a tuple
> or list containing the lengths and angles.
>
> def triclinic(L):
> B = [[0,0,0],[0,0,0],[0,0,0]]
>
> x, y, z, a, b, c = L[:6]
>
> B[0][0] = x
> if a == 90 and b == 90 and c == 90:
> B[1][1] = y
> B[2][2] = z
> else:
> a = a*pi/180
> b = b*pi/180
> c = c*pi/180
> B[1][0] = y*cos(c)
> B[1][1] = y*sin(c)
> B[2][0] = z*cos(b)
> B[2][1] = z*(cos(a)-cos(b)*cos(c))/sin(c)
> B[2][2] = sqrt(z*z-B[2][0]**2-B[2][1]**2)
>
> return B
>
> Hope it helps,
>
> Tsjerk
>
> On Tue, Feb 2, 2010 at 9:23 PM, Erik Marklund <erikm at xray.bmc.uu.se>
> wrote:
> > Hi,
> >
> > Since any unit cell can be formulated as a triclinic cell, the monoclinic
> > cell is indeed supported. By definition it has two 90 degree angles and
> one
> > that is not 90 degrees. The box vectors can be of different lengths.
> You'll
> > have to do the math and reading yourself to find out how this translates
> to
> > a .gro box. The manual is your friend here.
> >
> > Good luck,
> >
> > Erik
> >
> > Vishal Agarwal skrev:
> >>
> >> Dear Justin,
> >>
> >> Thanks for replying. The table mentions only a few unit cell type. I am
> >> using a monclinic unit cell. Do you know how these box vectors have been
> >> derived.
> >>
> >> thanks
> >> vishal
> >>
> >> On Tue, Feb 2, 2010 at 11:26 AM, Justin A. Lemkul <jalemkul at vt.edu
> >> <mailto:jalemkul at vt.edu>> wrote:
> >>
> >>
> >>
> >> Vishal Agarwal wrote:
> >>
> >> Dear gmx-users,
> >>
> >> I am new to GROMACS. Can anyone tell me what does the last
> >> line in .gro file stands for ?
> >>
> >> The manual mentions
> >> "box[X][X],box[Y][Y],box[Z][Z],
> >> box[X][Y],box[X][Z],box[Y][X],box[Y][Z],box[Z][X],box[Z][Y]"
> >>
> >> Can anyone explain what each of these mean in terms of cell
> >> parameters ?
> >>
> >>
> >> The last line contains the box vectors. Specifics in terms of
> >> unit cell geometry are given in the manual, Table 3.1 and section
> >> 3.2.1.
> >>
> >> -Justin
> >>
> >> Thanks,
> >> vishal
> >>
> >>
> >> -- ========================================
> >>
> >> Justin A. Lemkul
> >> Ph.D. Candidate
> >> ICTAS Doctoral Scholar
> >> MILES-IGERT Trainee
> >> Department of Biochemistry
> >> Virginia Tech
> >> Blacksburg, VA
> >> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >>
> >> ========================================
> >> -- gmx-users mailing list gmx-users at gromacs.org
> >> <mailto:gmx-users at gromacs.org>
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
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> >>
> >>
> >>
> >>
> >> --
> >> Regards
> >>
> >> ***********************************************
> >> Vishal Agarwal
> >> Research Scholar
> >> University of Massachusetts, Amherst
> >> ***********************************************
> >> 'Your only obligation in any lifetime is to be true to yourself."
> >> ---Richard Bach
> >
> >
> > --
> > -----------------------------------------------
> > Erik Marklund, PhD student
> > Laboratory of Molecular Biophysics,
> > Dept. of Cell and Molecular Biology, Uppsala University.
> > Husargatan 3, Box 596, 75124 Uppsala, Sweden
> > phone: +46 18 471 4537 fax: +46 18 511 755
> > erikm at xray.bmc.uu.se http://xray.bmc.uu.se/molbiophys
> >
> > --
> > gmx-users mailing list gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
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> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> Computational Chemist
> Medicinal Chemist
> Neuropharmacologist
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>
--
Regards
***********************************************
Vishal Agarwal
Research Scholar
University of Massachusetts, Amherst
***********************************************
'Your only obligation in any lifetime is to be true to yourself."
---Richard Bach
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