Oh, I just changed the [-cs spc216.gro] to [-cp spc216.gro] and this is working normally...??!! Do you have any idea?
On Sun, Oct 11, 2009 at 1:52 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Jamie Seyed wrote: > >> I converted spc216.pdb to gro using editconf. SO they must be the >> > > I suppose that's fine, I just don't see all the need for interconverting > file formats. It just opens up the possibility of more errors if you don't > keep track of what you're doing :) > > same(?). The version is 4.0.5 ...it was fine before... yes ran it just now >> for fws tuto... how long it takes time in your machine? >> > > I have the same version. The commands you showed completed in just a > fraction of a second, like most simple solvation procedures. > > -Justin > > >> On Sun, Oct 11, 2009 at 1:33 PM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> jalem...@vt.edu>> wrote: >> >> >> >> Jamie Seyed wrote: >> >> Hi Justin, >> yes resize.gro is a created file from editconf which has box >> size of 5.05918 on the last line >> my command was "editconf -bt cubic -f spc216.pdb -o resize.gro -d >> 1" >> >> >> Do you actually have separate spc216.pdb and spc216.gro files? Just >> trying to make sure this actually worked. >> >> >> and for second command I changed 1 to 5 but it still stops in >> the same point. I am trying to examine 2 methods that you & Mark >> suggested me to >> >> >> Very weird. Both of your commands worked on my machine. What >> version of Gromacs are you using? Does genbox work for other systems? >> >> -Justin >> >> create a box of water.../Many Thanks/Jamie >> >> On Sun, Oct 11, 2009 at 12:54 PM, Justin A. Lemkul >> <jalem...@vt.edu <mailto:jalem...@vt.edu> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote: >> >> >> >> Jamie Seyed wrote: >> >> Dear Gmx users, >> Does any one know why genbox stops when I use this command: >> "genbox -cp resize.gro -cs spc216.gro -o b4em.pdb -p >> topol.top" >> or when I use this command: >> "genbox -cs spc216.gro -box 1 1 1 -maxsol 500 -o out.gro -p >> topol.top" >> It goes until >> Reading solvent configuration >> Solvent configuration contains 648 atoms in 216 residues >> and then stops.... >> Would you please let me know why it happens?? Many Thanks in >> Advance/Jamie >> >> >> Is "resize.gro" a new file? Or something you have created >> before >> (i.e., an empty file with a box size defined)? >> >> Defining -box 1 1 1 generates a 1-nm cubic box, which is almost >> certainly too small to contain 500 solvent molecules. Define an >> appropriate box size. >> >> -Justin >> >> >> On Sun, Oct 11, 2009 at 12:04 PM, Jamie Seyed >> <jamie.se...@gmail.com <mailto:jamie.se...@gmail.com> >> <mailto:jamie.se...@gmail.com <mailto:jamie.se...@gmail.com>> >> <mailto:jamie.se...@gmail.com >> <mailto:jamie.se...@gmail.com> <mailto:jamie.se...@gmail.com >> <mailto:jamie.se...@gmail.com>>>> >> >> wrote: >> >> Thanks to Justin & Mark for answering my second >> question... >> Could any one give me a hint on my first question that >> I copy >> it again? >> --about g_velacc and calculating the diffusion >> constant from >> that. >> In mailing list people say that we need to divide it >> by mass >> squared >> and 1/3. Then I found another recent post that said it >> has been >> included in the code... Would you please clarify this >> that if >> I need >> the factors or not. Also I found 2 numbers after >> integration. >> >> Integral 1 0.01595 >> set average >> SS1 3.718082e-04 >> Would you please inform me what are these number and >> what is the >> relation between them? >> Many Thanks in Advance/Jamie >> >> On Sat, Oct 10, 2009 at 8:39 PM, Justin A. Lemkul >> <jalem...@vt.edu <mailto:jalem...@vt.edu> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>> wrote: >> >> >> >> Jamie Seyed wrote: >> >> Dear Gmx Users, >> I have a 2 questions. First about g_velacc and >> calculating >> the diffusion constant from that. In mailing list >> people say >> that we need to divide it by mass squared and >> 1/3. Then I >> found another recent post that said it has been >> included in >> the code... Would you please clarify this that >> if I >> need the >> factors or not. Also I found 2 numbers after >> integration. >> Integral 1 0.01595 >> set average >> SS1 3.718082e-04 >> --1) Would you please inform me what are these >> number and >> what is the relation between them? >> Can't comment on the first >> part...maybe the code will >> point you >> in the right direction? >> >> >> --2) My second question is I want to make a >> box of only >> water (spce) with let say 500 water molecules. >> Would you >> please give me quick hints how to do it (the >> proper >> way) or >> refer me to good point? Up to now I can only >> have 216 >> water >> molecules from tuto/water folder and I tried a >> lot >> >> >> This task might be approached in a couple of ways: >> >> 1. genconf -nbox to define a suitable number of >> replicate >> systems. >> 2. genbox -box -maxsol 500 to define a >> suitably-sized box and >> fill it with only the desired number of molecules. >> >> -Justin >> >> to start from the beginning, but I could not >> make it... I >> appreciate if you help me to understand the first >> issue and >> be able to overcome the second one. Many Thanks >> in >> Advance/Jamie >> >> >> >> ------------------------------------------------------------------------ >> >> >> >> _______________________________________________ >> gmx-users mailing list >> gmx-users@gromacs.org <mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org >> >> >> <mailto:gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org >> <mailto: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 >> <mailto:gmx-users-requ...@gromacs.org> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>>>. >> >> 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 gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org >> >> >> <mailto:gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org >> <mailto: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 <mailto: >> gmx-users-requ...@gromacs.org> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>>>. >> >> Can't post? Read >> http://www.gromacs.org/mailing_lists/users.php >> >> >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org <mailto: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 >> <mailto:gmx-users-requ...@gromacs.org> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>>. >> 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 gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>> >> 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 gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>>. >> 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 gmx-users@gromacs.org >> <mailto: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 >> <mailto:gmx-users-requ...@gromacs.org>. >> 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 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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