Vaclav Horacek wrote:
Hi Hazizian,
I have done md simulation of a 2-domain protein in water,
in 50 K but every
time I did it these domains are separated from each other,
and dont correct
when I do trjconv -pbc nojump,
This also happened to me once, since it can be impossible to correct the
trajectory with nojump once the protein goes through the periodic boundaries.
If I recall right, the solution was to use 'comm_mode' and 'comm_grps' in the
*.mdp file to ensure that the protein stays in the middle of the cell and does
not cross a boundary.
Using comm_grps other than "System" for a protein in water can lead to spurious
collisions and is not appropriate. Using trjconv is the proper way to fix this
issue. If -pbc nojump does not work, another option likely will. For me -pbc
mol -ur compact (and/or -center on the protein) works every time.
-Justin
Hope that helped,
Vaclav
--- On Sun, 10/18/09, hazizian <[email protected]> wrote:
From: hazizian <[email protected]>
Subject: [gmx-users] protein domain separation
To: [email protected]
Date: Sunday, October 18, 2009, 7:38 AM
Hi
I have done md simulation of a 2-domain protein in water,
in 50 K but every
time I did it these domains are separated from each other,
and dont correct
when I do trjconv -pbc nojump,
previous time when I did em or pr by doing trjconv -pbc
nojump, it
corrected.
The 50.mdp file is:
title
= n.pdb
cpp
= /lib/cpp
constraints =
none
integrator = md
dt
= 0.001
nsteps
= 100000
constraint_algorithm = shake
shake_tol =
0.0001
nstcomm
= 1
comm_mode
= Angular
nstxout
= 250
nstvout
= 1000
nstfout
= 0
nstlog
= 10
nstenergy
= 10
nstlist
= 10
ns_type
= grid
rlist
= 1.2
coulombtype =
PME
rcoulomb =
1.2
rvdw
= 1.4
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order
= 4
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on in three groups
Tcoupl
= berendsen
tau_t
= 0.4
0.4
tc-grps
= protein non-protein
ref_t
= 50
50
; Pressure coupling is on
Pcoupl
= berendsen
tau_p
= 2
compressibility = 4.5e-5
ref_p
= 1.0
; Generate velocites is on at 50 K.
gen_vel
= yes
gen_temp =
50.0
gen_seed =
173529
are they realy separated or I should do a command to
correct it, I search in
mailing list and could not find the result, please guide
me, thank you in
advance.
--
Tehran University of Medical Sciences
www.tums.ac.ir
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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