[email protected] wrote:
Dear all,
I am trying to put a chain of polyleucine in water - hexane interface.
Now after putting the chain of the peptide there are some overlaps. To
get rid of those overlaps I tried to run a MD with the position of
polyleucine constant (or restrained). But during energy minimization the
polyleucine is coming out of the interface. I generated the posre.itp
file with "genrestr" command and defined position restrain in the en.mdp
file. My en.mdp file is as follows.......
You are almost certainly seeing an artefact of periodic boundary
conditions. If not, please describe your observations more fully (e.g.
pictures) - "coming out of the interface" is quite vague. See
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
Mark
cpp = /lib/cpp
;include = -I posre.itp
define = -DPOSRES
; RUN CONTROL PARAMETERS =
integrator = steep
; start time and timestep in ps =
tinit = 0
dt = 0.001
nsteps = 10000
; ENERGY MINIMIZATION OPTIONS =
emtol = 0.00001
emstep = 0.1
nstcgsteep = 1000
and also posre.itp is included in the topology as follows
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
I dont want the polyleucine to come out of the interface. Please help.
Happy New Year to you all.
Prithvi
--
gmx-users mailing list [email protected]
http://lists.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
