[gmx-users] A question about deuteriu order parameters graph

Tue Nov 8 21:40:21 CET 2011

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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