Hi everyone, Today, I was attempting a simulation of a system with a lipid bilayer, and the size of my simulation box, obtained from a previous simulation, was 15 nm x 7.5 nm x 7.5 nm (15 nm being the direction perpendicular to the plane of the bilayer). The bilayer consisted of 128 DOPC lipids and was located at the centre of the box. I used periodic boundary conditions in all three directions.
I then resized the box to 7.5 nm in all directions, using the editconf -box option. After doing the requisite energy minimization steps, I ran the simulation using mdrun. However, running the simulation caused the box to gradually shrink in the y-direction (parallel to the plane of the bilayer!) during the simulation, ultimately settling at around half the original dimension. Is there anything I may have done that could cause this effect? I'm thoroughly baffled. Thanks! Regards Bharath -- Bharath K Srikanth IV Year B.Tech Dept. of Chemical Engineering Indian Institute of Technology, Guwahati Ph: (+91) 88762 03224 E.mail: s.bhar...@iitg.ernet.in -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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
