Hi Justin, Does it mean each time I can add one until I get the number that I want...?? Many Thanks/Jamie
On Thu, Aug 13, 2009 at 2:13 PM, Justin A. Lemkul <[email protected]> wrote: > > > Jamie Seyed wrote: > >> Hi Justin, >> I made an insert.gro file for 2 water molecules, and when I used genbox I >> got a fatal error: more than one residue in insert molecules, program >> terminated. >> > > Right, like I said before, the insert.gro file should contain coordinates > for *one* molecule. > > I wanted to look at insert.gro, it does not show anything. And when I >> convert it to pdb I got a warning [file aminoacids.dat, line 1]: Bad box >> file insert.gro >> > > Well, how did you make this file? A .gro file has a specific format: > > http://manual.gromacs.org/current/online/gro.html > > When I looked at the insert.pdb file I found only 1.5 water molecule! Which >> means 1 water plus a OH. Do you have any idea what should I do or if I am >> missing some thing? Many Thanks in Advance/Jamie >> >> > I have no idea how you created this broken file, so I can't really comment > :) The easiest thing to do (I would think) would be to take the first > molecule of spc216.gro, keep the header lines, set number of atoms = 3 and > preserve the box information at the bottom. I've used that before in a few > cases. > > -Justin > > On Thu, Aug 13, 2009 at 1:20 PM, Justin A. Lemkul <[email protected]<mailto: >> [email protected]>> wrote: >> >> >> >> Jamie Seyed wrote: >> >> Hi Justin, >> Thanks for your answer, >> On Thu, Aug 13, 2009 at 11:42 AM, Justin A. Lemkul >> <[email protected] <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>>> wrote: >> >> >> >> Jamie Seyed wrote: >> >> Dear all, >> 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 >> >> >> (1) The -vdwd option may help, or even -ci -nmol. If you have a >> pore, wouldn't water diffuse in over time anyway during >> equilibration (assuming an otherwise correct setup and realistic >> physical model)? >> >> Long time ago I did an experiment on water in confined geometry >> and I want to see if the results can obtain from the >> simulation... So for using -nmol -ci (at random position), it >> says I must use a file like insert.gro would you please explain >> me how I can make insert.gro? >> >> >> The "insert.gro" file contains the coordinates of one molecule that >> you want to insert, i.e. one water molecule. >> >> -Justin >> >> (2) If you haven't re-positioned your system within the box, it >> probably doesn't make any sense. The Gromacs convention is >> to place >> the corner of the box at the coordinate origin, and >> everything else >> is relative to that. Is a 1-nm cubic box large enough to >> encompass >> your system? If not, genbox is doing what it's told - filling a >> 1-nm box near the origin, and leaving everything else out. >> >> >> >> -Justin >> >> changing the box size will give a opposite result. Please >> advise..Thanks in advance/Jamie >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list [email protected] >> <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>> >> >> 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 [email protected] >> <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>>. >> >> Can't post? Read >> http://www.gromacs.org/mailing_lists/users.php >> >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu/> <http://vt.edu/> | (540) >> 231-9080 >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> _______________________________________________ >> gmx-users mailing list [email protected] >> <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>> >> >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/searchbefore >> posting! >> Please don't post (un)subscribe requests to the list. Use the >> www >> interface or send it to [email protected] >> <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>>. >> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> _______________________________________________ >> gmx-users mailing list [email protected] >> <mailto:[email protected]> >> 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 [email protected] >> <mailto:[email protected]>. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > _______________________________________________ > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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