On Thu, 2006-04-27 at 18:30 +1000, Mark Abraham wrote: > > > > In God We Trust > > Hello GMX users > > I want to use gromacs program to study a protein in a solvent of the > > mixture > > of 30% methanol and 70% water. Would you please tell me how can I make > > gro > > file of "mix solvent" box for genbox. > > There's no straightforward approach that I'm aware of. One possibility is > to do the arithmetic for the size box you want to use and generate a > smaller box filled with N water molecules that will give you 70% were you > to increase the size of the box and fill the gaps with methanol. Then > increase the size of the box, and use the -nmol and -ci options to genbox > to add enough methanols to make the mix 70/30. Then you will need to > equilibrate that box for a while to get a good mix of solvents at > reasonable density and pressure. I think you should be able to use that > box later for subsequently doing genbox for your protein. > > You could also manually delete enough waters to get down to 70%, and use > the genbox options above to try to fill the gaps, but you will have a hard > time fitting methanol into water-sized holes. > > Mark
How about using trjorder on the system before manually removing waters down to 70%. In that way it's easy to delete the ones most distant from the protein, leaving a continuous void in which methanol molecules are more easily inserted. You will end up with a inhomogenous solvent for sure, but it probably get mixed very quickly. Erik Marklund, PhD student Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > 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 mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users 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
