Hi Justin, My aim is to add water inside the pore (I do not care about outside), so as you told me I used the first line of spc216.gro and I do not know why after the calculations that I posted before it says segmentation fault?? Thanks in advance/Jamie
On Thu, Aug 13, 2009 at 2:41 PM, Justin A. Lemkul <[email protected]> wrote: > > > Jamie Seyed wrote: > >> Hi Justin, >> Does it mean each time I can add one until I get the number that I >> want...?? Many Thanks/Jamie >> >> > No need to do it manually. That's what -nmol is for. > > -Justin > > On Thu, Aug 13, 2009 at 2:13 PM, Justin A. Lemkul <[email protected]<mailto: >> [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]> >> <mailto:[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]>> >> <mailto:[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] >> >> >> <mailto:[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]>> >> <mailto:[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/> >> <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] >> >> >> <mailto:[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]>> >> <mailto:[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 >
_______________________________________________ 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
