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 <vvcha...@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 > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
