<div>Hi Vitaly,</div>
<div>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...</div>
<div>I did:</div>
<div>(1)editconf -bt cubic -f conf.gro -o pore_edco.pdb -d 0.02 ---> seems fine</div>
<div>(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.</div>
<div> </div>
<div>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...</div>
<div>I appreciate to get more information and some help... Thanks a lot/Jamie </div>
<div><br><br> </div>
<div class="gmail_quote">On Thu, Aug 13, 2009 at 12:21 PM, Vitaly V. Chaban <span dir="ltr"><<a href="mailto:vvchaban@gmail.com">vvchaban@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Jamie,<br><br>I didn't understand why you meant saying "waters far from the outside<br>of the pore"... Far from outside, then where exactly? Maybe I just<br>
imagine your box incorrectly.<br><br>To fill the pore with a solvent try to "deceive" genbox a little:<br>1) make a box (see editconf) in such a way that it contains only<br>"inside" part of your pore. genbox will not report an error from its<br>
side.<br>2) add the solvent with genbox.<br>3) return to the original box size.<br>4) add the outside part.<br><br>Vitaly<br>
<div class="im"><br>> I want to know how can I use genbox to fill inside of the pore as well as a<br>> layer outside. From the "man genbox" page I try to use -shell with a<br>> negative value (?) but it put waters far from the outside of the pore and I<br>
> think it does not care about the sign. It seems strange to me because when I<br>> had 10 10 10 in the last line of my f.gro, by a shell 0.5 or 0.2, I got a<br>> layer of few molecule around the pore, but when I change it to 1. 1. 1., the<br>
> water molecules generated far away. I appreciate if someone tell me (1) how<br></div>> I can add water inside the pore and (2) why changing the box size will give<br>
<div>
<div></div>
<div class="h5">> a opposite result. Please advise..Thanks in advance/Jamie<br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
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