After inserting the protein, the equilibrium box length in the x and y dimension should be different, so you need anisotropic pressure coupling during the 1st step. After equilibrium, the ratio of box length in x,y is fixed, so you can use semi-isotropic method.
--Jianguo ________________________________ From: Shima Arasteh <shima_arasteh2...@yahoo.com> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Sent: Friday, 17 August 2012, 7:26 Subject: [gmx-users] Protein-POPC bilayer Hi, I have a question about the Protein-POPC system: To insert a protein in lipid bilayer, I am suggested to simulate POPC in water separately before insertion, it might decrease the time of final simulation. It's OK! In the article suggested me by dear Peter C. Lai, I read that POPC was simulated in anisotropic pressure coupling at first and then after insertion of protein, semi-isotropic pressure coupling is applied. Now, would you please telling me why you used this procedure? And, Would my system be correct if I use semi-isotropic pressure coupling instead of anisotropic pressure coupling for the first step? Thanks in advance for your replies. Sincerely, Shima -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
