> What might be worth trying is starting with genconf. Use genconf -nbox (and > -dist, if necessary), starting from one MeOH molecule to generate a grid of > 400. > Then use genbox with -maxsol (and perhaps playing a bit with box > dimensions). > > -Justin
Thanks for your perspective, I really appreciate it I was trying around with that when I finally thought of a viable solution on my own, which actually seems to work (still simulating)... I'll put it here because I didn't find anything on the archives about creating mixed solvent systems and it may be of use to somebody: --> start with small box of given ratio (10 molecules 2moh:8water using single molecule moh.gro and spc216.gro from gmx top directory) genbox -ci moh.gro -nmol 2 -box 1 -o test.pdb -seed 5 genbox -cp test.pdb -cs spc216.gro -maxsol 8 -o test2.pdb --> set density lower than expected value to avoid clashes editconf -f test2.pdb -o test3.pdb -density 800 --> solvate system using small box as solvent genbox -cs test3.pdb -box 3.9 -o test4.pdb --> adjust box size so more than the necessary molecules are in the box --> MANUALLY delete surplus molecules in the coordinate file editconf -f test4.pdb -o 200moh_800wat.gro -density 950 --> set proper density to experimental values I haven't analyzed the result but at least the clashes are finally gone. I suppose boxes like this need to be equalibrated for a long time to insure a random distribution of molecules. _______________________________________________________________________ EINE FÜR ALLE: die kostenlose WEB.DE-Plattform für Freunde und Deine Homepage mit eigenem Namen. Jetzt starten! http://unddu.de/[EMAIL PROTECTED] _______________________________________________ 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
