[gmx-users] Re: density profile

[Elisabeth]

Thanks Vitaly. I am wondering what is the use of semiisotropic with 0
compressibility in Z then? I was hoping to run NPT to secure a fixed
pressure.

I also wanted to know if surface tension can be also calculated under NVT
(if NPT fails for this puporse)

Thanks!

On 31 March 2013 14:01, Dr. Vitaly Chaban <vvchaban at gmail.com> wrote:

> > Thanks Justin for your reply. To avoid compressing down the cell I
> thought
> > using semiisotropic option with 0 compressibility in Z would be
> > appropriate.
> >
> >
>
> You must use NVT only. Otherwise, the cell will compress in XY directions
> to compensate its inability to compress in Z direction.
>
>
>
>
> > 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
> >
> > My questions are:
> >
> > 1) Can I get the proper solvent-air interface to obtain density profile
> by
> > extending the Z direction (last line of the gro file obtained from NPT at
> > each pressure)? Is that what yo mean by " then build a new unit cell and
> > run under NVT" ?
> >
>
>
>
> If you want solvent/air interface, you should add $air.
>
> If you want solvent/vacuum interface, it is enough to extend the box.
>
> If you want liquid/vapor interface, you need to re-equilibrate the system
> in NVT with a space for vapor available in the box.
>
>
> Dr. Vitaly Chaban
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