Hi Alex
You're running just 1ns, which is actually too short for production in
this kind of systems. Enlarge the simulation time (e.g. up to 50ns) and
see if you get a more reasonable Scd plots.
Javier
El 08/11/11 21:40, Alex Jemulin escribió:
Dear Javier
Here is mdp file for MD run
title = cxcr7-DPPC Production MD
;
Run parameters
integrator = md ; leap-frog integrator
nsteps = 500000 ; 2 * 500000 = 1000 ps (1 ns)
dt = 0.002 ; 2 fs
;
Output control
nstxout = 1000 ; save coordinates every 2 ps
nstvout = 1000 ; save velocities every 2 ps
nstxtcout = 1000 ; xtc compressed trajectory output every 2 ps
nstenergy = 1000 ; save energies every 2 p
nstlog = 1000 ; update log file every 2 ps
; Bond parameters
continuation = yes ; Restarting after NPT
constraint_algorithm = lincs ; holonomic
constraints
constraints = all-bonds ; all bonds (even heavy atom-H
bonds) constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid ; search neighboring grid cels
nstlist = 5 ; 10 fs
rlist = 1.2 ; short-range neighborlist cutoff (in nm)
rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)
rvdw = 1.2 ; short-range van der Waals cutoff (in nm)
;
Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range
electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = Nose-Hoover ; More accurate thermostat
tc-grps = Protein DPPC SOL_NA ; three coupling groups -
more accurate
tau_t = 0.5 0.5 0.5 ; time constant, in ps
ref_t = 323 323 323 ; reference temperature,
one for each group, in K
;
Pressure coupling is on
pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT
pcoupltype = semiisotropic ; uniform scaling of x-y box
vectors, independent
z
tau_p = 2.0 ; time constant, in ps
ref_p = 1.0 1.0 ; reference pressure, x-y, z
(in bar)
compressibility = 4.5e-5 4.5e-5 ; isothermal compressibility, bar^-1
;
Periodic boundary conditions
pbc = xyz ; 3-D PBC
;
Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
;
Velocity generation
gen_vel = no ; Velocity generation is off
; COM motion removal
; These options remove motion of the protein/bilayer relative to the
solvent/ions
nstcomm = 1
comm-mode = Linear
comm-grps = Protein_DPPC SOL_NA
Here are some graphs I made after MD run:
g_energy -f md_0_1.edr -o temperature_MD.xvg
http://www.freeimagehosting.net/ca04e
g_energy -f md_0_1.edr -o pressione_MD.xvg
http://www.freeimagehosting.net/d3387
g_energy -f md_0_1.edr -o totenergia_MD.xvg
http://www.freeimagehosting.net/108a7
Here are commands for calculating deuterium order parameters
make_ndx -f md_0_1.tpr -o sn1.ndx
> a C34
> a C36
> a C37
> a C38
...
> a C50
> del 0-21
> q
g_order -s md_0_1.tpr -f md_0_1.xtc -n sn1.ndx -d z -od deuter_sn1.xvg
make_ndx -f md_0_1.tpr -o sn2.ndx
carbons C17-C31
del 0-21
q
g_order -s md_0_1.tpr -f md_0_1.xtc -n sn2.ndx -d z -od deuter_sn2.xvg
Thank your very much for your support
Bests
------------------------------------------------------------------------
*Da:* Javier Cerezo <[email protected]>
*A:* [email protected]
*Inviato:* Martedì 8 Novembre 2011 9:45
*Oggetto:* Re: [gmx-users] A question about deuteriu order parameters
graph
Hi Alex
Deuterium order parameter is a property related to the relative
orientation of molecular axis taking the bilayer normal as reference.
How to use them to extract useful structural information is a matter
of how you interpret the values regarding their definition (see e.g.
Egberts and Berendsen [J. Chem. Phys.(1988), vol 89, 3718] or Heller
et al [J. Phys. Chem. (1993), vol 97, 8343]). In general, by comparing
order parameters of different systems you can have some hints about
the phase or ordering of your different systems and how it may change
(for example at different temperature or after insertion of a membrane
protein).
Morover, the usefulness of this paramenter mainly comes from the fact
that they are readily available from simulations and thus can be used
to validate your methodology. Concretely, experimental information
about the deuterium order parameter (Scd, the one you reported) is
spread over the scientific literature about membranes (see e.g. the
series of papers from the J.F Nagle's group) and it is the deuterium
order parameter commonly reported in MD simulations. For the case of
DPPC you can take for example the ones from Petrache et al [Biophys. J
(2000), vol 79, 3172] and Douliez et al [Biophys. J. (1995), vol 68,
1727]. Take into account that GROMACS g_order tool just numerate your
atoms in the order the order parameters are calculated: the first Scd
comes from the second atom in the index, per the calculation
procedure, so is the CH2 close to the carbonyl (normally numbered as 2
in the chain).
In your case, if you compare your graphs with the experimental ones
(pure bilayers), they are significantly different, which may arise
from the fact of the protein insertion (I doubt it, however) or
indicate an incorrect MD calculation (bad parameters, not well
converged...) or incorrect Scd calculation. Please, post your MD
details (FF, mdp file...) and how you calculated the Scd to continue
the discussion. Did you calculate the Scd on the pure bilayer?
Javier
El 08/11/11 06:41, Alex escribió:
> Dear All,
>
> I run a MD simulation on a membrane protein using DPPC and I performed a
> deuterium order parameters on the trajectory.
> As I'm a newbie, could you kindly help me to give an interpretation
of these
> graphs?
>
> You can open them at:
> sn1
> http://www.freeimagehosting.net/137c9
>
> sn2
> http://www.freeimagehosting.net/6e321
>
>
> Thanks in advance
>
-- Javier CEREZO BASTIDA
PhD Student
Physical Chemistry
Universidad de Murcia
Murcia (Spain)
Tlf.(+34)868887434
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--
Javier CEREZO BASTIDA
PhD Student
Physical Chemistry
Universidad de Murcia
Murcia (Spain)
Tlf.(+34)868887434
--
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