As far as i remember for PBC the distance between the reference and the
pulled group are relevant, and not the distance between the reference
group and the virtual spring (place where the pulling potential is zero).
Looking into the code of GROMACS-4.0.7 backs this.
If the distance between the reference group and spring would be
relevant, one should see first an increasing force, then when pbc
matters, the force should decrease, because we pull now in the other
direction.
Looking into the code of GROMACS-4.5.4, it seems there is an error
message for pbc violations:
gmx_fatal(FARGS,"Distance of pull group %d (%f nm) is larger than 0.49
times the box size (%f)",g,sqrt(dr2),max_dist2);
pull.c; line 329
One thing is that the force constant for the pulling is quite small, so
probably you need more force the move the ligand? (But i can't really
comment on this, because i can't find your force vs time plot, so i
don't know how large the force actually is).
Greetings
Thomas
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
As you can see the pulling distance is 5 nm. The lenght of my box in Z
direction is 12 nm. Thus, it is not. Any other ideas?
No, it's not. You're doing 1 ns of simulation (contrary to the comment, 500000
* 0.002 = 1000 ps) and thus pulling at 10 nm per ns you are trying to pull 10 nm
in this simulation. So once your molecule hits 6 nm (right at about 600 ps from
your plot and the expected pull rate), you're violating the criterion that I
suspected.
-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>
<mailto: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>
<mailto: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>
<mailto: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>>
<mailto: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
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu<http://vt.edu>
<http://vt.edu/>
<http://vt.edu/> | (540) 231-9080
<tel:%28540%29%20231-9080>
<tel:%28540%29%20231-9080>
<tel:%28540%29%20231-9080>
http://www.bevanlab.biochem.
<http://www.bevanlab.biochem./__>____vt.edu/Pages/Personal/__justin
<http://vt.edu/Pages/Personal/justin>
<http://vt.edu/Pages/Personal/__justin
<http://vt.edu/Pages/Personal/justin>>
<http://www.bevanlab.biochem.____vt.edu/Pages/Personal/justin
<http://vt.edu/Pages/Personal/justin>
<http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>>>
==============================______==========
-- gmx-users mailing list
gmx-users@gromacs.org<mailto:gmx-users@gromacs.org>
<mailto:gmx-users@gromacs.org<mailto:gmx-users@gromacs.org>>
<mailto:gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
<mailto:gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>__>
http://lists.gromacs.org/______mailman/listinfo/gmx-users
<http://lists.gromacs.org/____mailman/listinfo/gmx-users>
<http://lists.gromacs.org/____mailman/listinfo/gmx-users
<http://lists.gromacs.org/__mailman/listinfo/gmx-users>>
<http://lists.gromacs.org/____mailman/listinfo/gmx-users
<http://lists.gromacs.org/__mailman/listinfo/gmx-users>
<http://lists.gromacs.org/__mailman/listinfo/gmx-users
<http://lists.gromacs.org/mailman/listinfo/gmx-users>>>
Please search the archive at
http://www.gromacs.org/______Support/Mailing_Lists/Search
<http://www.gromacs.org/____Support/Mailing_Lists/Search>
<http://www.gromacs.org/____Support/Mailing_Lists/Search
<http://www.gromacs.org/__Support/Mailing_Lists/Search>>
<http://www.gromacs.org/____Support/Mailing_Lists/Search
<http://www.gromacs.org/__Support/Mailing_Lists/Search>
<http://www.gromacs.org/__Support/Mailing_Lists/Search
<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
<mailto:gmx-users-requ...@gromacs.org>
<mailto:gmx-users-request@__gromacs.org
<mailto:gmx-users-requ...@gromacs.org>>
<mailto:gmx-users-request@
<mailto:gmx-users-request@>__gr__omacs.org<http://gromacs.org>
<mailto:gmx-users-request@__gromacs.org
<mailto:gmx-users-requ...@gromacs.org>>>.
Can't post? Read
http://www.gromacs.org/______Support/Mailing_Lists
<http://www.gromacs.org/____Support/Mailing_Lists>
<http://www.gromacs.org/____Support/Mailing_Lists
<http://www.gromacs.org/__Support/Mailing_Lists>>
<http://www.gromacs.org/____Support/Mailing_Lists
<http://www.gromacs.org/__Support/Mailing_Lists>
<http://www.gromacs.org/__Support/Mailing_Lists
<http://www.gromacs.org/Support/Mailing_Lists>>>
------------------------------____----------------------------__--__------------
------------------------------____----------------------------__--__------------
--
==============================____==========
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>
<http://vt.edu/> | (540) 231-9080<tel:%28540%29%20231-9080>
<tel:%28540%29%20231-9080>
http://www.bevanlab.biochem.____vt.edu/Pages/Personal/justin
<http://vt.edu/Pages/Personal/justin>
<http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>>
==============================____==========
-- gmx-users mailing list
gmx-users@gromacs.org<mailto:gmx-users@gromacs.org>
<mailto:gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>
http://lists.gromacs.org/____mailman/listinfo/gmx-users
<http://lists.gromacs.org/__mailman/listinfo/gmx-users>
<http://lists.gromacs.org/__mailman/listinfo/gmx-users
<http://lists.gromacs.org/mailman/listinfo/gmx-users>>
Please search the archive at
http://www.gromacs.org/____Support/Mailing_Lists/Search
<http://www.gromacs.org/__Support/Mailing_Lists/Search>
<http://www.gromacs.org/__Support/Mailing_Lists/Search
<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
<mailto:gmx-users-requ...@gromacs.org>
<mailto:gmx-users-request@__gromacs.org
<mailto:gmx-users-requ...@gromacs.org>>.
Can't post? Read
http://www.gromacs.org/____Support/Mailing_Lists
<http://www.gromacs.org/__Support/Mailing_Lists>
<http://www.gromacs.org/__Support/Mailing_Lists
<http://www.gromacs.org/Support/Mailing_Lists>>
------------------------------__------------------------------__------------
--
==============================__==========
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>
http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
==============================__==========
--
gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
http://lists.gromacs.org/__mailman/listinfo/gmx-users
<http://lists.gromacs.org/mailman/listinfo/gmx-users>
Please search the archive at
http://www.gromacs.org/__Support/Mailing_Lists/Search
<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
<mailto:gmx-users-requ...@gromacs.org>.
Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists
<http://www.gromacs.org/Support/Mailing_Lists>
--
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
