What is the box size and what is the cutoff displayed by genbox?
On Thu, Aug 13, 2009 at 8:10 PM, Jamie Seyed<jamie.se...@gmail.com> wrote: > Hi Vitaly, > Thanks for the answer. When I said far away means my pore was in one corner > of vmd window and the water molecules in opposite corner (almost). Anyways, > I tried to use your method but I think I am missing some parts... > I did: > (1)editconf -bt cubic -f conf.gro -o pore_edco.pdb -d 0.02 ---> seems fine > (2)genbox -cp pore_edco.pdb -cs spc216.gro -o pore edco_b4em.pdb -p > topol.top here there is an error: one of the box vectors has become shorter > than twice the cut-off length or box_yy-|box_zy| or box_zz has become > smaller than the cut-off. > > would you please let me know how I can fix the error (I don't see where I > can change the cut-off !). Also am I doing right or I need a box of water > first without introducing my molecule... > I appreciate to get more information and some help... Thanks a lot/Jamie > > > On Thu, Aug 13, 2009 at 12:21 PM, Vitaly V. Chaban <vvcha...@gmail.com> > wrote: >> >> Jamie, >> >> I didn't understand why you meant saying "waters far from the outside >> of the pore"... Far from outside, then where exactly? Maybe I just >> imagine your box incorrectly. >> >> To fill the pore with a solvent try to "deceive" genbox a little: >> 1) make a box (see editconf) in such a way that it contains only >> "inside" part of your pore. genbox will not report an error from its >> side. >> 2) add the solvent with genbox. >> 3) return to the original box size. >> 4) add the outside part. >> >> Vitaly >> >> > I want to know how can I use genbox to fill inside of the pore as well >> > as a >> > layer outside. From the "man genbox" page I try to use -shell with a >> > negative value (?) but it put waters far from the outside of the pore >> > and I >> > think it does not care about the sign. It seems strange to me because >> > when I >> > had 10 10 10 in the last line of my f.gro, by a shell 0.5 or 0.2, I got >> > a >> > layer of few molecule around the pore, but when I change it to 1. 1. 1., >> > the >> > water molecules generated far away. I appreciate if someone tell me (1) >> > how >> > I can add water inside the pore and (2) why changing the box size will >> > give >> > a opposite result. Please advise..Thanks in advance/Jamie _______________________________________________ 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/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/mailing_lists/users.php
