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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