it is because when i put genbox -cp protein_box.gro -ci solvent.gro -nmol 1381 -p control.top -o prot_solv.gro
the error turn out like this : System total charge: 0.000 Grid: 17 x 16 x 14 cells nri = 12718, nrj = 100152 Try 9119box_margin = 0.45overlap: Killed thats why i need to run genbox twice On Mon, Oct 8, 2012 at 9:21 AM, Justin Lemkul [via GROMACS] <[email protected]> wrote: > > > On 10/7/12 9:17 PM, shika wrote: > >> Thanks Justin. >> >> May I ask something, if i'm using the command for genbox before >> minimization which is >> >> genbox -cp protein_box.gro -cs solvent.gro -p control.top -o prot_solv.gro >> >> next i insert water by using same command; >> >> genbox -cp prot_solv.gro -p control.top -cs spc216.gro -o >> prot_solv_wtr.gro maxsol 350 >> >> i'm using -cs for both genbox command instead of -ci -nmol, is it >> wrong to use the command like that? >> >> > > I don't understand why you need two invocations of genbox, but syntactically > the > commands are correct. The -ci -nmol options are for adding molecules > randomly > in the unit cell. The -cs option is for stacking grids of water boxes (or > whatever other solvent you provide) within the unit cell. > > -Justin > >> >> >> On Mon, Oct 8, 2012 at 8:59 AM, Justin Lemkul [via GROMACS] >> <[hidden email]> wrote: >>> >>> >>> On 10/7/12 3:52 PM, Ali Alizadeh wrote: >>>> Dear All users >>>> >>>> How to can i replace a molecule(for example methane) with another >>>> molecule(propane)? >>>> Number of these molecules are given and their position is random, >>>> >>>> Can I use genbox or genion, How to do i do it? >>>> >>> >>> Likely you can't, as you were already advised: >>> >>> http://lists.gromacs.org/pipermail/gmx-users/2012-October/075338.html >>> >>> A more robust approach for dealing with mixed systems can be found here: >>> >>> http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents >>> >>> -Justin >>> >>> -- >>> ======================================== >>> >>> Justin A. Lemkul, Ph.D. >>> Research Scientist >>> 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 [hidden email] >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>> * Please don't post (un)subscribe requests to the list. Use the >>> www interface or send it to [hidden email]. >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> >>> ________________________________ >>> If you reply to this email, your message will be added to the discussion >>> below: >>> >>> http://gromacs.5086.n6.nabble.com/How-to-can-i-replace-a-molecule-tp5001756p5001764.html >>> To start a new topic under GROMACS Users Forum, email >>> [hidden email] >>> To unsubscribe from GROMACS, click here. >>> NAML >> >> >> > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > 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 [hidden email] > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [hidden email]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > ________________________________ > If you reply to this email, your message will be added to the discussion > below: > http://gromacs.5086.n6.nabble.com/How-to-can-i-replace-a-molecule-tp5001756p5001768.html > To start a new topic under GROMACS Users Forum, email > [email protected] > To unsubscribe from GROMACS, click here. > NAML -- Best Regards, Nur Syafiqah Abdul Ghani, Theoretical and Computational Chemistry Laboratory, Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, 43400 Serdang, Selangor. 013-7188131 alternative email : [email protected] -- View this message in context: http://gromacs.5086.n6.nabble.com/How-to-can-i-replace-a-molecule-tp5001756p5001770.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
