> 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
