Dear All, I have a system of a crystal slab at the center of the box surrounded by water. I am using position restraints for crystal. I am observing a weird thing that after NPT equilibration of system populated with SPC water using gromacs genbox command, some kinda hole or vacuum appears in the water layers. Let me explain with the snapshots that can be accessed from following link:
https://www.dropbox.com/sh/jms49mz5w409d5p/AACUx7ek7x91Rvv0yiVW2cPEa Image 1 shows equilibrated snapshot of system with "all" as refcoord scaling option and water NOT from genbox command, but instead inserted manually. As we can see, there are no holes/vacuum in the box. Images 2 and 3 show the holes in the water layers. refcoord scaling option "all" is used and crystal is solvated by SPC water, latter generated using genbox command. Image 4 shows equilibrated snapshot of system where "com" option is used for refcoord scaling, and crystal is populated with SPC water from genbox command. As we see, there is a displacement of the slab from center to left, but there are no holes/vacuum in the water layers. Thus, combination of all option and genbox SPC population is problematic for some reason. Noting that slab does not move with "all" option, whereas it does move with "com" option, there is some issue with SPC water generation using genbox in gromacs. Also, I am using following settle algorithm for constraining water geometry: [ settles ] ; i funct length-oh length -hh 1 1 0.1 0.16333 Could anyone shed light? Thanks a lot! regards Chetan -- 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.