[gmx-users] surface tension-density profile

[Elisabeth]

Deal all,

I am trying to build up my alkane system to calculate the surface tension a
fixed pressure. Here are the steps:

1- First I did a 10 ns NPT to equilibrate the box and used the last frame
gro and cpt file as input for the next step
2- I extended the box in Z to more than twice the initial box size and
issued the following:

grompp -f md.mdp -c extendedZ.gro -t .cpt -p .top -o extendedZ.tpr
mpirun -np 4 mdrun_mpi -deffnm .extendedZ -s -o -c -g -e -x -v

However, I am not clear about the setting of pressure coupling and
compressibility. I guess I need to use 0 compressibility in Z with
isotropic option?

Please advise me on the settings and details of these calculations. I am
going to compare the surface tension and density profiles at several
different pressures.

Thank you in advance :)


Below is the md.mdp contents:

pbc                 =  xyz


integrator          =  md

dt                  =  0.001

nsteps              =  20000000

nstcomm             =  100



;           Output control

nstenergy           =  100

nstxout             =  100;1

 nstvout             =  0

nstfout             =  0

nstlog              =  1000

nstxtcout           =  1000

;           Neighbor searching

nstlist             =  10

ns_type             =  grid

;           Electrostatics/VdW

coulombtype         =  Shift

vdw-type            =  Shift

rcoulomb-switch     =  1

rvdw-switch         =  1 ;0.9

;           Cut-offs

rlist               =  1.35

rcoulomb            =  1.1   ;1.1

rvdw                =  1.1


Tcoupl              =  v-rescale

tc-grps             =  System

tau_t               =  0.1

ref_t               =  425

*   *

*Pcoupl              =  berendsen*

*Pcoupltype          =  isotropic                 *

*tau_p               =  1      0.5                *

*compressibility     =  3.5e-5 3.5e-5 0*

*ref_p               =  50   10** *



gen_vel             =  no

gen_temp            =  500.0

gen_seed            =  173529



constraints         = none

constraint-algorithm = lincs