[gmx-users] A question about deuteriu order parameters graph
Javier Cerezo
jcb1 at um.es
Wed Nov 9 09:17:22 CET 2011
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 <jcb1 at um.es>
> *A:* gmx-users at gromacs.org
> *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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