Chih-Ying Lin wrote:
Hi
How to make a solution with specific concentration ?
Concentration of what? For ions, use genion -conc; for other solute molecules,
do some simple stoichiometry from General Chemistry based on the box volume.
Command 1 =>
editconf -d 0.75 -bt cubic
0.75=Distance between the solute and the box
cubic = the type of the simulation box
Command 2 =>
genbox -cp solute.gro -cs spc.gro -box Y Y Y
Y = the box vector in nm
If I use cubic in my system, is Y defined as the length of the cubic in
the three directions?
Yes, that's what you've instructed genbox to do.
Is the overall volume of the simulation box = Y * Y *Y (nm*nm*nm) ?
Yes.
Is the center of cubic on the origin (0,0,0) of the coordinate?
No. By convention, the system will be centered at (Y/2) in each direction.
If you're setting up your system using the above commands, it might be easier to
just combine the box creation into one step with editconf (which will also print
the coordinates of the system center): editconf -bt cubic -box Y -c
-Justin
Thank you
Lin
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php