[gmx-users] Solvent_box
Tsjerk Wassenaar
tsjerkw at gmail.com
Thu Jul 12 19:51:26 CEST 2007
Hi Prasenjit,
Okay, this one's more clear in regards your objective (should've read
my mail in chronological order). Your problem is basically the
handling of PBC itself.
The trick is to give a center with the option -center, and to apply
this to the first atom of the solute. Note that gromacs always places
the solute such that the first atom is inside the central box (the one
located at the origin). So, place it just a bit from the edge, such
that the solute is positioned correctly as a starting point for
pulling.
I hope this is a bit clear...
Cheers,
Tsjerk
On 7/12/07, pkmukher <pkmukher at olemiss.edu> wrote:
> Hi users,
>
> To answer Mark's question about reading section 3.2. Yes I
> have.I wish to conduct an SMD study.I want to place my
> protein system at one end of the longest side of triclinic
> shell and then pull parallel to the longest side.
>
> Yang I have used both pymol and VMD for visualization
>
> Tsjerk when i dont use the -d option the box is created with
> the protein completely outside the box and at a distance. I
> was therefore thinking of either the -d option or -c option.
> I dont want to center my protein in the box but keep it as
> far as possible (allowing buffer) on one side of the
> rectangle so that I can pull through the solvent using
> SMD..for the editconf i get a message that the box type was
> not defined although i have given -bt triclinic.
>
> see below
>
> r1028 at redwood:~/bcl2/solvation> editconf -f two.pdb -o
> three.pdb -d 0.9 -box 20 10 10 -bt triclinic
> :-) G R O M A C S (-:
>
> Getting the Right Output Means no Artefacts in
> Calculating Stuff
>
> :-) VERSION 3.3.1 (-:
>
>
> Written by David van der Spoel, Erik Lindahl, Berk
> Hess, and others.
> Copyright (c) 1991-2000, University of Groningen, The
> Netherlands.
> Copyright (c) 2001-2006, The GROMACS
> development team,
> check out http://www.gromacs.org for more
> information.
>
> This program is free software; you can redistribute
> it and/or
> modify it under the terms of the GNU General
> Public License
> as published by the Free Software Foundation;
> either version 2
> of the License, or (at your option) any later
> version.
>
> :-) editconf (-:
>
> Option Filename Type Description
> ------------------------------------------------------------
> -f two.pdb Input Generic structure: gro g96
> pdb tpr tpb tpa
> xml
> -n index.ndx Input, Opt. Index file
> -o three.pdb Output, Opt! Generic structure: gro g96
> pdb xml
> -mead mead.pqr Output, Opt. Coordinate file for MEAD
> -bf bfact.dat Input, Opt. Generic data file
>
> Option Type Value Description
> ------------------------------------------------------
> -[no]h bool no Print help info and quit
> -nice int 0 Set the nicelevel
> -[no]w bool no View output xvg, xpm, eps and
> pdb files
> -[no]ndef bool no Choose output from default index
> groups
> -bt enum triclinic Box type for -box and -d:
> triclinic, cubic,
> dodecahedron or octahedron
> -box vector 20 10 10 Box vector lengths (a,b,c)
> -angles vector 90 90 90 Angles between the box vectors
> (bc,ac,ab)
> -d real 0.9 Distance between the solute and
> the box
> -[no]c bool no Center molecule in box (implied
> by -box and -d)
> -center vector 0 0 0 Coordinates of geometrical
> center
> -translate vector 0 0 0 Translation
> -rotate vector 0 0 0 Rotation around the X, Y and Z
> axes in degrees
> -[no]princ bool no Orient molecule(s) along their
> principal axes
> -scale vector 1 1 1 Scaling factor
> -density real 1000 Density (g/l) of the output box
> achieved by
> scaling
> -[no]vol bool yes Compute and print volume of the
> box
> -[no]pbc bool no Remove the periodicity (make
> molecule whole
> again)
> -[no]grasp bool no Store the charge of the atom in
> the B-factor
> field and the radius of the atom
> in the occupancy
> field
> -rvdw real 0.12 Default Van der Waals radius (in
> nm) if one can
> not be found in the database or
> if no parameters
> are present in the topology file
> -sig56 real 0 Use rmin/2 (minimum in the Van
> der Waals
> potential) rather than sigma/2
> -[no]vdwread bool no Read the Van der Waals radii
> from the file
> vdwradii.dat rather than
> computing the radii
> based on the force field
> -[no]atom bool no Force B-factor attachment per
> atom
> -[no]legend bool no Make B-factor legend
> -label string A Add chain label for all residues
>
> WARNING: masses will be determined based on residue and atom
> names,
> this can deviate from the real mass of the atom
> type
> In case you use free energy of solvation predictions:
>
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> D. Eisenberg and A. D. McLachlan
> Solvation energy in protein folding and binding
> Nature 319 (1986) pp. 199-203
> -------- -------- --- Thank You --- -------- --------
>
> Opening library file
> /usr/local/appl/gromacs-3.3.1/share/gromacs/top/aminoacids.dat
> Opening library file
> /usr/local/appl/gromacs-3.3.1/share/gromacs/top/atommass.dat
> Opening library file
> /usr/local/appl/gromacs-3.3.1/share/gromacs/top/vdwradii.dat
> Opening library file
> /usr/local/appl/gromacs-3.3.1/share/gromacs/top/dgsolv.dat
> #Entries in atommass.dat: 82 vdwradii.dat: 26 dgsolv.dat: 7
> Read 1307 atoms
> Volume: 0.001 nm^3, corresponds to roughly 0 electrons
> No velocities found
> system size : 4.956 4.351 4.507 (nm)
> center : -0.412 -0.852 -0.082 (nm)
> box vectors : 0.100 0.100 0.100 (nm)
> box angles : 90.00 90.00 90.00 (degrees)
> box volume : 0.00 (nm^3)
> shift : 3.790 3.928 3.236 (nm)
> new center : 3.378 3.075 3.154 (nm)
> new box vectors : 6.756 6.151 6.307 (nm)
> new box angles : 90.00 90.00 90.00 (degrees)
> new box volume : 262.11 (nm^3)
>
> WARNING: No boxtype specified - distance condition applied
> in each dimension.
> If the molecule rotates the actual distance will be smaller.
> You might want
> to use a cubic box instead, or why not try a dodecahedron
> today?
>
> Back Off! I just backed up three.pdb to ./#three.pdb.1#
>
> gcq#289: "Do You Have a Mind of Your Own ?" (Garbage)
>
> Prasenjit Kumar Mukherjee
> Graduate Student
> Department of Medicinal Chemistry
> School of Pharmacy
> University of Mississippi
> USA
>
> Cell - 662 380 0146
> Office - 662 915 1286
>
>
>
>
>
>
>
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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