[gmx-users] Re: genbox generating acetonitrile box with holes

[Vitaly Chaban]

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.chaban at rochester.edu
University of Rochester      |  email: vvchaban at gmail.com
Rochester, NY 14627-0216     |  email: chaban at 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