Maurício Menegatti Rigo wrote:
Hi,
I'm facing a problem with GROMACS that appears pretty simple, actually.
I'm trying to set a dodecahedron box but all I can get is a triclinic
box. For that, I'm using the following line:
/
editconf -f pMHC -bt dodecahedron -o -d 1 /
Am I doing something wrong?? Another problem, different from this one,
There is no problem. Whatever visualization software you're using is assembling
the box as a triclinic representation. You can post-process your trajectory
using "trjconv -pbc mol -ur compact" to see the real representation.
is that my protein, during the simulation, is escaping/comming
off/"running away" (sorry I'm butchering the english) from the water
box. I tried to use periodic boundaries conditions, but didn't work (I
added a line in my .mdp file - pbc = xyz). Someone could help me with
that, please?
Your protein is also not coming out of the box; it is a normal consequences of
periodicity (which is, in fact, working just fine):
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
-Justin
I really appreciate !
--
Maurício Menegatti Rigo
Núcleo de Bioinformática do Laboratório de Imunogenética
Departamento de Genética
Instituto de Biociências
Universidade Federal do Rio Grande do Sul - Brazil
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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