[gmx-users] Re: density profile

[Dr. Vitaly Chaban]

> 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