Hey, Diana - I believe these acetonitrile holes are not a problem. Just perform an equilibration run in the NPT ensemble and they will disappear. The more tricky way is to adjust VDW radii in vdwradii.dat before using genbox.
By the way, what force field model of acetonitrile do you use here? Some time ago I uploaded a few simulation boxes with acetonitrile onto the gromacs official website, hopefully they can be also useful for you to start. Good luck! Dr. Vitaly V. Chaban | skype: vvchaban Department of Chemistry | email: v.cha...@rochester.edu University of Rochester | email: vvcha...@gmail.com Rochester, NY 14627-0216 | email: cha...@univer.kharkov.ua United States of America | WWW: chem.rochester.edu/~prezhdo_group/index.php/members/5-vitaly-chaban > I am trying to solvate a protein in a box of acetonitrile using genbox. My > initial solvent box is a cubic box containing 300 molecules of acetonitrile > that has been equilibrated for 500 ps at constant P and T. > > I used the following protocol to generate the box: > ####################################################################################### > #create the box > editconf -f protein.pdb -d 1.2 -o protein_in_box.pdb -bt dodecahedron > > #solvate > genbox -cp protein_in_box.pdb -cs acetonitrile_eq.gro -o > protein_in_acetonitrile.gro > > #convert the box to visualize it > touch empty.mdp > > grompp -f empty.mdp -c protein_in_acetonitrile.gro -p > 01_make_top/protein_ACN.top > trjconv -f protein_in_acetonitrile.gro -o protein_in_acetonitrile.pdb -pbc > atom -ur compact <<EOF > 0 > EOF > ####################################################################################### > > After these steps I get a box that has holes and I can't understand why. > > I couldn't send the final pdb file in attachment, if anyone thinks he/she > can help and whishes to see the pdb file I will send it to your email. > > Thanks in advance. > > Diana > > -- > Diana Lousa > PhD student > Protein Modeling Laboratory > ITQB/UNL > Oeiras, Portugal -- 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
