Dear David: If the two leaflets are moving with respect to each other (along the bilayer plane), then why would this be artificial? I have also seen this (diffusive) motion, and in addition to wondering why you would call it artificial, it seems to me that the motion would have to be many orders of magnitude larger than is observed in simulations for it to affect the temperature. Subtracting the COM of each leaflet separately is not only impossible, but inadvisable.
Chris. -- original message -- I ran into similar issues for a DPPC bilayer. It might be possible that the two leaflets of the bilayer are moving with respect to eachother. If this is not taken into account, these artificial velocities will mean the simulation thinks it is at a higher temperature than it really is. If possible, you might want to try subtracting the center of mass motion of each leaflet, rather than the center of mass motion of the entire bilayer. This will allow the system to equillibrate to the correct (higher) temperature, and should increase the area per lipid of the bilayer. Hope this helps. -David -- 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
