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
On Sun, Oct 11, 2009 at 12:04 PM, Jamie Seyed <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>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 >>> 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 >>> >> >> -- >> ======================================== >> >> 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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