Hi Simone, I would advise you to insert the needed number of waters (genbox -cp conf.gro -cs water.gro -o conf1.gro) and then do the same with DMSO ((genbox -cp conf1.gro -cs dmso.gro -o conf2.gro). Then just equilibrate.
Vitaly > > I need to run a simulation of a protein in a water/DMSO mixture. I can't > quite understand how should I do this... should I normally solvate the > protein with water and then replace a certain number of water molecules > (according to the needed % of DMSO) with DMSO molecules? But in this case, > how should I do it? Is there a way of replacing solvent molecules with other > solvent molecules, but of a different type? > I'm sorry but I don't know which procedure to follow. > Thanks in advance _______________________________________________ gmx-users mailing list [email protected] http://lists.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
