Hi, I'm not accustomed with coarse grained, but from the little stuff I know on MD in order to keep a box's size constant you have to use an NVT simulation not an NPT. Meaning don't keep pressure constant but rather the volume. Do double check though, I might be wrong.
________________________________________ From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of HongTham <hongtham0...@gmail.com> Sent: Friday, May 29, 2015 9:13 AM To: gmx-us...@gromacs.org Subject: [gmx-users] (no subject) Dear Gromacs User, I simulated a coarse grained membrane protein system. This is my pressure control parameter. ; pressure control Pcoupl = berendsen ; Pcoupltype = semiisotropic ; tau-p = 5.0 5.0 ; compressibility = 4.5e-5 4.5e-5 ; ref-p = 1.0 1.0 1.0 1.0 ; refcoord_scaling = all ; Although I set Pcoupltype as semiisotropic, after running simulation a while, my box was changed from cubic (starting) to rectangular parallelepiped. the x,y direction were shortened while z direction was lengthened a lot. is there any option to control the box size through the simulation? Thank you so much. Hongtham -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
