Re: [gmx-users] How to build boxes with constant number of solvent molecules?
Peyman Yamin wrote: Hello dears, I want to solvate different conformations of a molecule in a water box and I want to have the same number of solvent molecules in my box at the end. I do it with genbox but end up with different number of solvent molecules. A random insertion of more molecules results in a box which would not be easily equilibrated. I also tried to solvate in a larger box and then delete some molecules from the end of file so that I have a certain number of molecules for all of them, but it also results in a strange looking environments in the box which mostly lead to an equilibration crash. Does one know any practical strategy to solvate a molecule in a box and have the number of solvent molecules fixed?? I appreciate any suggestions, regards, Peyman genbox -maxsol -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-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
[gmx-users] How to build boxes with constant number of solvent molecules?
Hello dears, I want to solvate different conformations of a molecule in a water box and I want to have the same number of solvent molecules in my box at the end. I do it with genbox but end up with different number of solvent molecules. A random insertion of more molecules results in a box which would not be easily equilibrated. I also tried to solvate in a larger box and then delete some molecules from the end of file so that I have a certain number of molecules for all of them, but it also results in a strange looking environments in the box which mostly lead to an equilibration crash. Does one know any practical strategy to solvate a molecule in a box and have the number of solvent molecules fixed?? I appreciate any suggestions, regards, Peyman -- Peyman Yamin Lehrstuhl fuer Thermische Verfahrenstechnik Universitaet Erlangen-Nuernberg Egerlandstr. 3 91058 Erlangen Phone: +49(0) - 9131 - 85 27671 Mailto: [EMAIL PROTECTED] ___ gmx-users mailing listgmx-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
