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 >
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