Steven Neumann wrote:
Hello Justin,
As you recommended I run longer pulling of my ligand. I pull the ligand
which is on the top of my protein so the top of the protein is pulled so
that the whole protein rotated app. 30 degrees - the low part of the
protein came out of the box due to the rotation. After app 600 ps the
ligand does not move any more and the force applied increase linearly.
As I saw the trajectory, ligand does not collide with a periodic image
but it does not move. Please, see attacheg plot force vs time. Can you
explain why the force increase linearly and ligand is not pulled any
more? This is my mdp file for pulling:
Is the pulled distance greater than half of the box vector in z? That's the
only reason I can see things going haywire. With simple "distance" geometry,
there are some limitations like that. Rotation itself is not a problem. You're
separating two objects; there's no clear orientation dependence in that case.
-Justin
title = Umbrella pulling simulation
; Run parameters
integrator = md
dt = 0.002
tinit = 0
nsteps = 500000 ; 500 ps
nstcomm = 10
; Output parameters
nstxout = 5000 ; every 10 ps
nstvout = 5000
nstfout = 500
nstxtcout = 500 ; every 1 ps
nstenergy = 500
; Bond parameters
constraint_algorithm = lincs
constraints = all-bonds
continuation = yes ; continuing from NPT
; Single-range cutoff scheme
nstlist = 5
ns_type = grid
rlist = 0.9
rcoulomb = 0.9
rvdw = 0.9
; PME electrostatics parameters
coulombtype = PME
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc_grps = Protein_LIG Water_and_ions ; two coupling groups - more
accurate
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 298 298 ; reference temperature, one
for each group, in K
; Pressure coupling is on
Pcoupl = Parrinello-Rahman
pcoupltype = isotropic
tau_p = 1.0
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocities is off
gen_vel = no
; Periodic boundary conditions are on in all directions
pbc = xyz
; Long-range dispersion correction
DispCorr = EnerPres
; Pull code
pull = umbrella
pull_geometry = distance ; simple distance increase
pull_dim = N N Y
pull_start = yes ; define initial COM distance > 0
pull_ngroups = 1
pull_group0 = Protein
pull_group1 = LIG182
pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns
pull_k1 = 200 ; kJ mol^-1 nm^-2
Would you recommend position restrained of the protein backbone atoms or
e.g. residues from the lower part so that the protien will not roatate?
Thank you,
Steven
On Fri, Feb 17, 2012 at 10:41 AM, Steven Neumann
<s.neuman...@gmail.com <mailto:s.neuman...@gmail.com>> wrote:
On Mon, Feb 13, 2012 at 2:53 PM, Steven Neumann
<s.neuman...@gmail.com <mailto:s.neuman...@gmail.com>> wrote:
Thank you Justin!
On Mon, Feb 13, 2012 at 2:44 PM, Justin A. Lemkul
<jalem...@vt.edu <mailto:jalem...@vt.edu>> wrote:
Steven Neumann wrote:
Thank you Justin. I run my pulling using two force
constant for pulling. K1=100 and K1=200
Please, see attached plots of force vs time. Is
there any criteria to adjust pulling constant? Would
you suggest running it for a longer time?
I know of no systematic study for choosing a force
constant. Guessing wildly at what's going on, I'd say
you need longer simulations as it appears you have only
just caused dissociation towards the end of the 500 ps.
-Justin
Steven
On Mon, Feb 13, 2012 at 1:11 PM, Justin A. Lemkul
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>
wrote:
Steven Neumann wrote:
Dear Gmx Users,
Is it always required to restrained
positions of the protein
while pulling your ligand? My system is made
of 10 ligands
attached to my protein surface. I am pulling
one of them.
No, it is not required. I assume you've gotten
this idea from my
tutorial - the restraints there were used for a
very specific
purpose (detailed in the paper linked from the
tutorial).
I have just seen trajectory of pulling my
ligand without
restraining positions of protein and 9
remaining ligands. My
ligand while pulling also pulled the protein
with itself (for 1
nm distance) and then splited. Is is this
approach more reliable?
If your goal is umbrella sampling, you need only
generate a series
of reasonable starting configurations along a
defined reaction
coordinate. The absolute positions are
irrelevant; it is the
relative distance that matters.
-Justin
-- ==============================____==========
Justin A. Lemkul
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Department of Biochemistry
Virginia Tech
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<http://www.bevanlab.biochem./>____vt.edu/Pages/Personal/justin
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==============================__==========
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080
<tel:%28540%29%20231-9080>
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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
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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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