normal changing unsaturated tails and headgroups

  • syahidah
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11 years 9 months ago #999 by syahidah
Dear MARTINI users,

in tutorial 1d: changing lipid type for "unsaturated tail" section, it states that to replace dspc by dopc in .top and .mdp file, but how about the .gro file? may i use the single_dspc.gro but replace the "DSPC" to "DOPC" or we need to have new dopc.gro? because thereis no dopc.gro implemented in the tutorial..

in "changing the headgroup" how can we change the headgroups from PC to PE?

Furthermore, may i know the phenomenon of few lipid structures jumping in and out of the simulation box is normal or not?

may i know anyone here have any idea to solve the problem..?

Your reply is greatly appreciated

Thank You so much..

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11 years 9 months ago #1000 by djurre
Replied by djurre on topic changing unsaturated tails and headgroups
As long as the number of beads per lipid are the same (which is the case for DOPC and DSPC), you don't have to change the gro file. If you run grompp it will give you a warning ("There are non-matching atom names"). Ignore the warning and in the output .gro file the names will be changed.

For the lipids jumping in and out: they are probably not actually jumping, but just moving over the periodic box boundary. That is no problem. If don't want to see it anymore, you can run trjconv with option '-pbc atom'.

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11 years 9 months ago #1001 by syahidah
Replied by syahidah on topic changing unsaturated tails and headgroups
Dear djurre,
thank you so much for the reply, yes no more jumping atom=)

however when i want to analyze the g_density, the shape of the partial density graph that i get from my simulation is not the same with the result for the per-run.

the graph has few fluctuation unlike the pre-run density graph where it has two peak in smooth line..i wish i can show you the graph..

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11 years 9 months ago #1002 by djurre
Replied by djurre on topic changing unsaturated tails and headgroups
The fluctuation in the graph could be due to a lack of sampling (you simply do not have enough time/frames) or it might be the the bilayer is drifting through the box (in the Z-dimension). In second case you should make you sure you have separate COM motion removal for bilayer and water. Could one of those be the problem?

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11 years 9 months ago #1003 by syahidah
Replied by syahidah on topic changing unsaturated tails and headgroups
Thank you so much for the reply=)

Did you mean that i have to "-rmcomm" during the density analysis just like what is done in msd analysis?

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11 years 9 months ago #1004 by djurre
Replied by djurre on topic changing unsaturated tails and headgroups
I meant the COM options in the mdp file. g_analysis doesn't have an option rmcomm as far as I know.

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11 years 9 months ago #1005 by syahidah
Replied by syahidah on topic changing unsaturated tails and headgroups
dear djurre,

Thanks a lot for the suggestion, really appreciate that..
i'll try =)

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11 years 9 months ago #1027 by syahidah
Replied by syahidah on topic changing unsaturated tails and headgroups
Dear djurre,

As what you suggested before, i did seperate the DSPC and W
where the .mdp file was like below:

; STANDARD MD INPUT OPTIONS FOR MARTINI 2.1
;
; for use with GROMACS 4
;

; RUN CONTROL PARAMETERS
; MARTINI - Most simulations are stable with dt=40 fs, some (especially rings)
; require 20-30 fs.
; The range of time steps used for parametrization is 20-40 fs, using smaller
; time steps is therefore not recommended.
integrator = md
; Start time and timestep in ps:
tinit = 0.0
dt = 0.030
nsteps = 900000
; nsteps = 500000
; Number of steps for center of mass motion removal:
nstcomm = 1 1
comm-grps = DSPC W

; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f):
nstxout = 5000
nstvout = 5000
nstfout = 0
; Output frequency for energies to log (.log) file and energy (.edr) file:
nstlog = 1000
nstenergy = 1000
; Output frequency and precision for .xtc file:
nstxtcout = 1000
xtc_precision = 100

; NEIGHBORSEARCHING PARAMETERS
; MARTINI - No need for more frequent updates or larger neighborlist cut-off
; due to the use of shifted potential energy functions.
; Neighborlist update frequency:
nstlist = 10
; Neighbor searching algorithm (simple|grid):
ns_type = grid
; Periodic boundary conditions (xyz|none):
pbc = xyz
; Neighborlist cut-off:
rlist = 1.2

; OPTIONS FOR ELECTROSTATICS AND VDW
; MARTINI - VdW and electrostatic interactions are used in their shifted forms.
; Changing to other types of electrostatics will affect the general performance
; of the model.
; Method for doing electrostatics:
coulombtype = Shift
rcoulomb_switch = 0.0
rcoulomb = 1.2
; Dielectric constant (DC) for cut-off or DC of reaction field:
epsilon_r = 15
; Method for doing Van der Waals:
vdw_type = Shift
; Cut-off lengths:
rvdw_switch = 0.9
rvdw = 1.2
; Apply long range dispersion corrections for Energy and Pressure?
DispCorr = No

; OPTIONS FOR WEAK COUPLING ALGORITHMS
; MARTINI -Normal temperature and pressure coupling schemes can be used. It
; is recommended to couple individual groups in your system seperately.
; Temperature coupling:
tcoupl = berendsen
; Groups to couple separately:
tc-grps = DSPC W
; Time constant (ps) and reference temperature (K):
tau_t = 0.3 0.3
ref_t = 323 323
; Pressure coupling:
Pcoupl = berendsen
Pcoupltype = isotropic
; Pcoupltype = semiisotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar):
tau_p = 3.0
compressibility = 3e-5
ref_p = 1.0
; tau_p = 3.0 3.0
; compressibility = 3e-5 3e-5
; ref_p = 1.0 1.0

; GENERATE VELOCITIES FOR STARTUP RUN:
gen_vel = no
gen_temp = 320
gen_seed = 473529

; OPTIONS FOR BONDS
; MARTINI - For ring systems constraints are defined which are best handled
; using Lincs.
constraints = none
; Type of constraint algorithm:
constraint_algorithm = Lincs
; Do not constrain the start configuration:
unconstrained_start = no
; Highest order in the expansion of the constraint coupling matrix:
lincs_order = 4
; Lincs will write a warning to the stderr if in one step a bond rotates over
; more degrees than:
lincs_warnangle = 30


unlike before, this time i didn't get bilayer but spherical micelle..
did i insert wrong value?

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11 years 9 months ago #1029 by djurre
Replied by djurre on topic changing unsaturated tails and headgroups
The fact that it forms micelle could be just coincidence (bad luck). But that does mean you are starting from random placed lipids, which I didn't understand before. In a simulation forming the bilayer from a random configuration, i'm not sure if it makes sense to have the COM removal seperate.

I would first form the bilayer using one COM removal group and isotropic pressure coupling and then run a longer simulations using separate COM groups and semiisotropic pressure coupling (make sure the bilayer has formed in the XY-plane). Then calculate the density profile for the second, long simulation.

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11 years 9 months ago #1030 by syahidah
Replied by syahidah on topic changing unsaturated tails and headgroups
Dear djurre,

thank you sooo much for your explanation =),
actually, i'm doing the tutorial implemented in this homepage,
i followed the tutorial one by one,step by step..
when i want to analyze the partial density to get the thickness,
the distance from peak to peak is acceptable i think because it can be considered near to the given value, but instead of two peaks with smooth line, i got 2 high peaks (where i can take the distance for the thickness) and few small peaks in the middle (the line seems fluctuated)..
there are 3 people doing the similar tutorial without changing any commands, but our results are different, 2 of us got fluctuated (just like mine as i explained above) graph and another 1 got 2 peaks with sooth line just like a normal partial density graph.
i think the only difference among us is mine is 32bit and hers 64bit..

may i ask 1 more question, how can we calculate how many lipid in each leaflet using gromacs?

your reply is greatly appreciated..

thank you so much djurre..

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11 years 9 months ago #1031 by syahidah
Replied by syahidah on topic changing unsaturated tails and headgroups
Dear Djurre,

thank you so much for your suggestion and help,
finally, the density graph solved=).

Thank you=)

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