Hi Tsjerk, Thank you for this suggestion. It's a good idea to have previously equilibrated bricks then used for a main system.
Unfortunately, my the ratios between ion and solvent usually appear quite far from the integer because I have fixed concentration. Moreover, a CNT is present in the same system... :) The replication will not simplify the procedure in the present case. Does anybody have more ideas how to force all particles to be inserted without consecutive equilibrations? I tried to reduce -vdwd of the genbox but telling the truth, no difference was found (version 3.3.1). Thanks, Vitaly 2008/8/18 Tsjerk Wassenaar <[EMAIL PROTECTED]>: > Hi Vitaly, > > Do you have a rather fixed ratio between the two? ion:solvent = 1:10 > e.g. Then you could make an arrangement of a single ion with > surrounding solvent and replicate that with genconf. You could even do > a short simulation setting rvdw to less than half the size of your > small box :p for a bit of equilibration. > > Cheers, > > Tsjerk > > On Mon, Aug 18, 2008 at 10:29 AM, Vitaly Chaban > <[EMAIL PROTECTED]> wrote: >> Hi, >> >> I want to create a system (conf.gro) consisting of a solvent and >> polyatomic (brachiated enough) ions. >> >> Using genconf and genbox I increase the number of molecules and then >> ions (or contrariwise). But genbox refuses to add all the requested >> particles at once (because of intersections, I guess). What I do? - I >> add the number of ions it allows and make short md run. Then a few >> other particles can be added. Repeating the procedure several times, >> the system is ready. >> >> The question is how to avoid these tricks? How to initialize the >> system at once (even with intersections). Further, the energy >> minimization will be done before MD itself. Of course, by means of >> standard gromacs tools. >> >> >> Thanks. >> >> -- >> Vitaly V. Chaban >> School of Chemistry >> National University of Kharkiv >> Svoboda sq., 4, Kharkiv 61077, Ukraine >> email: [EMAIL PROTECTED] >> skype: vvchaban >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> http://www.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 >> > > > > -- > Tsjerk A. Wassenaar, Ph.D. > Junior UD (post-doc) > Biomolecular NMR, Bijvoet Center > Utrecht University > Padualaan 8 > 3584 CH Utrecht > The Netherlands > P: +31-30-2539931 > F: +31-30-2537623 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.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
