Re[3]: [gmx-users] size of the system

> The correct file to use is spc216.gro (which genbox automatically finds in > the GROMACS $GMXLIB/top directory). I'm guessing that genbox is finding a > local spc216.pdb which is somehow broken. Thanks a lot. I've fixed the problem translating ".pdb" to ".gro" It was really something wrong with .

Re[2]: [gmx-users] size of the system

It seems my answer to Berk was processes by the system in a wrong way. > guess this procedure should work, so this might be a bug. > But you are making things much more complicated than needed. > You can skip the first two steps and just use the -box option of genbox > instead of -cp. > > Berk.

Re[2]: [gmx-users] size of the system

JAL> the gcc 4.1.x compilers produce a broken product. It seems everything is OK with genbox (ver 3.1 and 3.3). When doing the same with any protein.pdb (+water from spc216.pdb) it works. The problem occurs only when I deal with any pure solvent. Vitaly __

Re[2]: [gmx-users] size of the system

> I guess this procedure should work, so this might be a bug. But you are making things much more complicated than needed. You can skip the first two steps and just use the -box option of genbox instead of -cp. Berk. OK.  genbox -cs spc216.pdb -box 3 3 3. It outputs:       Opti

[gmx-users] size of the system

Dear Colleagues, I've got a novice question as for GROMACS. For example, I need a system of 500 water molecules. Initially, I've spc216.pdb. Then I try: pdb2gmx -f spc216.pdb -o conf.pdb editconf -f conf.pdb -o box.pdb -d 0.7 genbox -cp box.pdb -cs spc216 -o water.pdb -p topol.top The utility outp