shahrbanoo karbalaee wrote:
Dear justin
I made a file with (n1/n2=30) two solvents.I want to equilbrate this
file.then I must minimize and run md(pre md ).please correct me if It
is not right.
I use
editconf -f test42.pdb(this file) -bt dodecahedron - d 0.5 -o box.gro
as you tell for delet periodicity
editconf -f box.pdb -princ -pbc -vdwread
I could minimiz it.and now I have a distorted file .how can steady
and smooth .
What do you mean distorted? The default output will be rendered such that it is
in a triclinic box, which can be corrected with trjconv -ur compact -pbc mol. I
have never found editconf -pbc to be entirely reliable.
-Justin
do you think I have to do long md for it or another else?
best and thank you
--
========================================
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
