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 >
_______________________________________________ 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