<div class="MsoPlainText" style="MARGIN: 0cm 0cm 0pt"><font face="Courier New">Hi Vitaly,</font></div>
<div class="MsoPlainText" style="MARGIN: 0cm 0cm 0pt"><font face="Courier New">This is after runing genbox:</font></div>
<div class="MsoPlainText" style="MARGIN: 0cm 0cm 0pt"><font face="Courier New">-----------------------------------</font></div>
<div class="MsoPlainText" style="MARGIN: 0cm 0cm 0pt"><font face="Courier New">opening library file /home/seyedyazdij/gromacs-4.0.5/share/top/aminoacids.dat<br>WARNING: masses will be determined based on residue and atom names,<br>
<span style="mso-tab-count: 1"> </span><span style="mso-spacerun: yes"> </span>this can deviate from the real mass of the atom type<br><span style="mso-tab-count: 1"> </span><span style="mso-spacerun: yes"> </span>Opening library file /home/seyedyazdij/gromacs-4.0.5/share/top/atommass.dat<br>
<span style="mso-tab-count: 1"> </span><span style="mso-spacerun: yes"> </span>Entries in atommass.dat: 178<br><span style="mso-tab-count: 1"> </span><span style="mso-spacerun: yes"> </span>WARNING: vdwradii will be determined based on residue and atom names,<br>
<span style="mso-tab-count: 2"> </span><span style="mso-spacerun: yes"> </span>this can deviate from the real mass of the atom type<br><span style="mso-tab-count: 2"> </span><span style="mso-spacerun: yes"> </span>Opening library file /home/seyedyazdij/gromacs-4.0.5/share/top/vdwradii.dat<br>
<span style="mso-tab-count: 2"> </span><span style="mso-spacerun: yes"> </span>Entries in vdwradii.dat: 28<br><span style="mso-tab-count: 2"> </span><span style="mso-spacerun: yes"> </span>Opening library file /home/seyedyazdij/gromacs-4.0.5/share/top/dgsolv.dat<br>
<span style="mso-tab-count: 2"> </span><span style="mso-spacerun: yes"> </span>Entries in dgsolv.dat: 7<br><span style="mso-tab-count: 2"> </span><span style="mso-spacerun: yes"> </span>Opening library file /home/seyedyazdij/gromacs-4.0.5/share/top/electroneg.dat<br>
<span style="mso-tab-count: 2"> </span><span style="mso-spacerun: yes"> </span>Entries in electroneg.dat: 71<br><span style="mso-tab-count: 2"> </span><span style="mso-spacerun: yes"> </span>Opening library file /home/seyedyazdij/gromacs-4.0.5/share/top/elements.dat<br>
<span style="mso-tab-count: 2"> </span><span style="mso-spacerun: yes"> </span>Entries in elements.dat: 218<br><span style="mso-tab-count: 2"> </span><span style="mso-spacerun: yes"> </span>Reading solute configuration<br>
<span style="mso-tab-count: 2"> </span><span style="mso-spacerun: yes"> </span>Fullereno in vacuum<br><span style="mso-tab-count: 2"> </span><span style="mso-spacerun: yes"> </span>Containing 60 atoms in 1 residues<br>
<span style="mso-tab-count: 2"> </span><span style="mso-spacerun: yes"> </span></font><font face="Courier New"><span lang="NL" style="mso-ansi-language: NL">Initialising van der waals distances...<br><span style="mso-tab-count: 2"> </span><span style="mso-spacerun: yes"> </span></span>Reading solvent configuration<br>
<span style="mso-tab-count: 2"> </span><span style="mso-spacerun: yes"> </span>"216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984"<br><span style="mso-tab-count: 2"> </span><span style="mso-spacerun: yes"> </span>solvent configuration contains 648 atoms in 216 residues<br>
<br><span style="mso-tab-count: 2"> </span><span style="mso-spacerun: yes"> </span></font><font face="Courier New"><span lang="NL" style="mso-ansi-language: NL">Initialising van der waals distances...<br><span style="mso-tab-count: 2"> </span><span style="mso-spacerun: yes"> </span></span>Will generate new solvent configuration of 1x1x1 boxes<br>
<span style="mso-tab-count: 2"> </span><span style="mso-spacerun: yes"> </span>Generating configuration<br><span style="mso-tab-count: 2"> </span><span style="mso-spacerun: yes"> </span>Sorting configuration<br>
<span style="mso-tab-count: 2"> </span><span style="mso-spacerun: yes"> </span>Found 1 molecule type:<br><span style="mso-tab-count: 2"> </span><span style="mso-spacerun: yes"> </span>SOL (<span style="mso-spacerun: yes"> </span>3 atoms):<span style="mso-spacerun: yes"> </span>216 residues<br>
<span style="mso-tab-count: 2"> </span><span style="mso-spacerun: yes"> </span>Calculating Overlap...<br><span style="mso-tab-count: 2"> </span><span style="mso-spacerun: yes"> </span>box_margin = 0.315<br>
<span style="mso-tab-count: 2"> </span><span style="mso-spacerun: yes"> </span>Removed 528 atoms that were outside the box<br><span style="mso-tab-count: 2"> </span><span style="mso-spacerun: yes"> </span><span style="mso-spacerun: yes"> </span>Neighborsearching with a cut-off of 0.45<br>
<span style="mso-tab-count: 2"> </span><span style="mso-spacerun: yes"> </span>Table routines are used for coulomb: FALSE<br><span style="mso-tab-count: 2"> </span><span style="mso-spacerun: yes"> </span>Table routines are used for vdw:<span style="mso-spacerun: yes"> </span>FALSE<br>
<span style="mso-tab-count: 2"> </span><span style="mso-spacerun: yes"> </span>Cut-off's:<span style="mso-spacerun: yes"> </span>NS: 0.45<span style="mso-spacerun: yes"> </span>Coulomb: 0.45<span style="mso-spacerun: yes"> </span>LJ: 0.45<br>
<span style="mso-tab-count: 2"> </span><span style="mso-spacerun: yes"> </span>System total charge: 0.000<br><br><span style="mso-tab-count: 2"> </span><span style="mso-spacerun: yes"> </span>-------------------------------------------------------<br>
<span style="mso-tab-count: 2"> </span><span style="mso-spacerun: yes"> </span>Program genbox, VERSION 4.0.5<br><span style="mso-tab-count: 2"> </span><span style="mso-spacerun: yes"> </span>Source code file: ns.c, line: 2295<br>
<br><span style="mso-tab-count: 2"> </span><span style="mso-spacerun: yes"> </span>Fatal error:<br><span style="mso-tab-count: 2"> </span><span style="mso-spacerun: yes"> </span>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.<br>
<span style="mso-tab-count: 2"> </span><span style="mso-spacerun: yes"> </span>-------------------------------------------------------</font></div>
<div class="MsoPlainText" style="MARGIN: 0cm 0cm 0pt"><font face="Courier New">Thanks in advance/Jamie</font><br></div><br><br>
<div class="gmail_quote">On Thu, Aug 13, 2009 at 2:10 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">What is the box size and what is the cutoff displayed by genbox?<br>
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<div class="h5"><br>On Thu, Aug 13, 2009 at 8:10 PM, Jamie Seyed<<a href="mailto:jamie.seyed@gmail.com">jamie.seyed@gmail.com</a>> wrote:<br>> Hi Vitaly,<br>> Thanks for the answer. When I said far away means my pore was in one corner<br>
> of vmd window and the water molecules in opposite corner (almost). Anyways,<br>> I tried to use your method but I think I am missing some parts...<br>> I did:<br>> (1)editconf -bt cubic -f conf.gro -o pore_edco.pdb -d 0.02 ---> seems fine<br>
> (2)genbox -cp pore_edco.pdb -cs spc216.gro -o pore edco_b4em.pdb -p<br>> topol.top here there is an error: one of the box vectors has become shorter<br>> than twice the cut-off length or box_yy-|box_zy| or box_zz has become<br>
> smaller than the cut-off.<br>><br>> would you please let me know how I can fix the error (I don't see where I<br>> can change the cut-off !). Also am I doing right or I need a box of water<br>> first without introducing my molecule...<br>
> I appreciate to get more information and some help... Thanks a lot/Jamie<br>><br>><br>> On Thu, Aug 13, 2009 at 12:21 PM, Vitaly V. Chaban <<a href="mailto:vvchaban@gmail.com">vvchaban@gmail.com</a>><br>
> wrote:<br>>><br>>> 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>>><br>>> > I want to know how can I use genbox to fill inside of the pore as well<br>
>> > 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<br>>> > and I<br>
>> > think it does not care about the sign. It seems strange to me because<br>>> > 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<br>>> > a<br>>> > layer of few molecule around the pore, but when I change it to 1. 1. 1.,<br>
>> > the<br>>> > water molecules generated far away. I appreciate if someone tell me (1)<br>>> > how<br>>> > I can add water inside the pore and (2) why changing the box size will<br>>> > give<br>
>> > 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><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
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