[gmx-users] About lipid simulation...

[rama david]

Hi Gromacs friends,

I am very novice to the lipid simulation study..
My problem may be very simple, But very imp to me to know it.

I am trying to  reproduced the result of article  ¨Antimicrobial
peptide in Action¨
Published in JACS, 2006,128, 12156-12161, doi no = 10.1021/ja062927q



As per article they used two conditions,

1. Stress free ( Lateral  Tension = 0)
2. Stress condition ( Lateral  tension = 20 mNm/m)

parameter for simulation as follow,

Weakly coupled temp 323 k ( Coupling time = 0.1)
Weakly coupled press ( Coupling time = 0.5 Compressibility 5 e-5 bar -1)

Keep the P|| ( lateral press ) and  Pz( Perpendicular press ) same
P||  = Pz = 1 ,
Result will be stress free bilayer ( Lateral  Tension = 0).

For other condition of P||  =   -30  Pz = 1 , result in a lateral tension of
20 mNm/m

for stress free condition I made following npt.mdp
; Temperature coupling is on
tcoupl        = Berendsen            ; More accurate thermostat
tc-grps        = Protein DPPC    SOL_CL    ; three coupling groups -
more accurate
tau_t        = 0.1    0.1    0.1            ; time constant, in ps
ref_t        = 323     323    323            ; reference temperature,
one for each group, in K
; Pressure coupling is on
pcoupl        =  Berendsen        ; Pressure coupling on in NPT
pcoupltype    = semiisotropic            ; uniform scaling of x-y box
vectors, independent z
tau_p        = 0.5                    ; time constant, in ps
ref_p        = 1.0    1.0                ; reference pressure, x-y, z (in bar)
compressibility = 5.0e-5    5.0e-5    ; isothermal compressibility, bar^-1


And for stress condition I made the following npt.mdp

; Temperature coupling is on
tcoupl        = Berendsen            ; More accurate thermostat
tc-grps        = Protein DPPC    SOL_CL    ; three coupling groups -
more accurate
tau_t        = 0.1    0.1    0.1            ; time constant, in ps
ref_t        = 323     323    323            ; reference temperature,
one for each group, in K
; Pressure coupling is on
pcoupl        =  Berendsen        ; Pressure coupling on in NPT
pcoupltype    = semiisotropic            ; uniform scaling of x-y box
vectors, independent z
tau_p        = 0.5                    ; time constant, in ps
ref_p        =  -30.0    1.0                ; reference pressure, x-y,
z (in bar)
compressibility = 5.0e-5    5.0e-5    ; isothermal compressibility, bar^-1


Please help to make right npt.mdp from above  mention parameter.


I read the Gromacs manual for 4.5.4, Section 3.4 page no 33,
Surface tension coupling work with only Berendsen Press coupling.

Please , would you tell me how to calculate lateral surface tension from
P|| ( lateral press ) and  Pz( Perpendicular press )  ???
( Why to say  P||  =   -30  Pz = 1 , will give the teral tension of
20 mNm/m  ???)


Please give me the valuable suggestion in these regard....

Thank you in advance.

Have a nice Day.
With best wishes and regards,


Rama David