ram bio wrote:
Dear Gromacs Users,
I am performing an all-atom simulation of protein ligand complex in
lipid bilayer , but after around 100ns, I see that the protein started
moving in one dimension in the lipid bilayer that is it is not in the
centre, I want the position of the protein fixed through out the
simulation, so pl suggest regarding this..
This is a normal consequence of diffusion in a periodic system. There is no
such thing as a "center." For visualization purposes, just post-process your
trajectory with trjconv.
and is it ok if I increase the position restraints for the protein by
changing the values of forces on x y and z dimensions in the posre.itp
file (below) of the protein, and if so how much can i increase the
force, so that i doesnot effect the simulation.
If you're trying to get around the diffusion issue, don't. If this is part of
equilibration, all you're doing is setting up a higher energy barrier for the
movement of these atoms. The difference between 1000 and 2000 should be
relatively minimal, as far as the end result is concerned.
-Justin
[ position_restraints ]
; atom type fx fy fz
1 1 2000 2000 2000
5 1 2000 2000 2000
7 1 2000 2000 2000
10 1 2000 2000 2000
13 1 2000 2000 2000
14 1 2000 2000 2000
18 1 2000 2000 2000
19 1 2000 2000 2000
20 1 2000 2000 2000
21 1 2000 2000 2000
23 1 2000 2000 2000
26 1 2000 2000 2000
29 1 2000 2000 2000
32 1 2000 2000 2000
33 1 2000 2000 2000
34 1 2000 2000 2000
35 1 2000 2000 2000
37 1 2000 2000 2000
40 1 2000 2000 2000
Thanks in advance,
Ram
--
========================================
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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
