I have tried with decane, octane and CCl4. The three of them got me the same problem, pressure scaling more than 1%. I have tried increasing the tau_p value, cause that was one of the solutions given in gmx user's list. That didn´t work out either. All my simulations were carried out using ffgmx forcield. I think the problem is due to using the wrong parameters in my input mdp files, but I don´t really know which. That is why I asked about some tutorial or something more especific about building protein boxes with apolar solvents. If I could choose, I would prefer using octane box with ffgmx forcefield cause I will eventually work with a lipid bilayer and will use such a forcefield in my simulations.
2009/2/17 Vitaly Chaban <[email protected]>: >>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 Fabrício, > > 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
