>Hello, I would like to know if there is any recommendation onto >setting up a system with a protein in a apolar solvent box. If there >is any tutorial or web page with topologies for solvents. I read that >the decane box that comes with gromacs is not to be used for >simulations, if that is true, then how should I assemble my system?
Hi FabrÃcio, It seems nothing is extremely specific in your task if the force field is ready. What solvent do you need? Is it really decane? I have never worked with decane topology provided with gromacs but I know there's some well-studied ones in the literature. Read about editconf and genbox standard gromacs utilities to make your box. Best, Vitaly -- Vitaly V. Chaban, Ph.D. (ABD) School of Chemistry National University of Kharkiv Svoboda sq., 4, Kharkiv 61077, Ukraine email: [email protected] skype: vvchaban _______________________________________________ gmx-users mailing list [email protected] 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
