[gmx-users] Bilayer area questions again!

[Rama Gullapalli]

Dear Dr Warren
Thanks for replying back. Here is the exact full.mdp
file which i used for the equilibriation of the
bilayer of 10 nanoseconds.
Thank you for your time and patience.
Sincerely
Regards
Rama

;
;	User spoel (236)
;	Wed Nov  3 17:12:44 1993
;	Input file
;
title               =  Yo
cpp                 =  /lib/cpp
constraints         =  all-bonds
integrator          =  md
dt                  =  0.002	; ps !
nsteps              =  5000000	; total 10 ps.
nstcomm             =  1
nstxout             =  10000
nstvout             =  10000
nstfout             =  0
nstlog              =  10000
nstenergy           =  10000
nstlist             =  10
ns_type             =  grid
dispcorr            =  enerpres
coulombtype         =  cut-off
rlist               =  1.0
rcoulomb            =  1.8
vdwtype             =  cut-off
rvdw                =  1.8
; Berendsen temperature coupling is on in two groups
Tcoupl              =  berendsen
tc-grps		    =  DPPC SOL
tau_t               =  0.1  0.1
ref_t               =  323  323	
; Energy monitoring
energygrps          =  DPPC  SOL
; Isotropic pressure coupling is now on
Pcoupl              =  berendsen
Pcoupltype          =  anisotropic
tau_p               =  5.0    
compressibility     =  4.5e-5 4.5e-5 4.5e-5 0.0 0.0
0.0
ref_p               =  1.0    1.0    1.0    0.0 0.0
0.0
; Generate velocites is off at 300 K.
gen_vel             =  no
gen_temp            =  300.0
gen_seed            =  173529


--- "Dallas B. Warren"
<Dallas.Warren at vcp.monash.edu.au> wrote:

> Rama,
> 
> Might help if you post your md.mdp file you are
> using here.
> 
> Simply sounds to me that there is no pressure
> coupling in the x-y plane,
> so the box stays pretty much the same dimensions.
> 
> Catch ya,
> 
> Dr. Dallas Warren
> Lecturer
> Department of Pharmaceutical Biology and
> Pharmacology
> Victorian College of Pharmacy, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.warren at vcp.monash.edu.au
> +61 3 9903 9073
> ---------------------------------
> When the only tool you own is a hammer, every
> problem begins to resemble
> a nail.
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