shahrbanoo karbalaee wrote:
Dear justin
a) if I want to have the steady and hemogen for mix solvent , do I
have to use this command (when I made genbox box 16.16.24 before
that)?
:editconf -f conf.gro -bt dodecahedron -d 0.5 -o box.gro
This will not homogenize anything; it only sets up the initial system. To get a
homogeneous box you have to equilibrate (sometimes for a very long time).
b) I use trjconv -pbc mol -ur compact and then minimize .when I see
the output this part in vmd or ngmx and around X-rotate.I will see
water in top and tfe in down box and another roatation the box is
seemed hemogen ous .is it correct?
No. Using -pbc mol -ur compact is a post-processing trick to visualize. If you
use the trjconv output in a simulation, it's likely to go screwy, since Gromacs
determines periodicity from a triclinic unit cell.
Create your system (using -bt dodecahedron is fine, but will likely look like a
rectangle in VMD or ngmx), and minimize. Use the output of the minimization for
your equilibration simulations. If you want to visualize a dodecahedral box,
then use trjconv, but do not use this altered file for simulations.
-Justin
about distortion ,my mean is"donot have periodicity and hemogenity"
thanks and appreiciate u
--
========================================
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
========================================
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