[gmx-users] PS_PC system

Justin A. Lemkul jalemkul at vt.edu
Mon Aug 22 15:14:01 CEST 2011

Du Jiangfeng (BIOCH) wrote:
> Dear Gromacs Users,
> I am still struggling with PS_PC system for quiet a long time. I want to
> distribute some DPPS lipids (Negative changed) in one leaflet of DSPC
> (Neutral) membrane, however, the PS lipids go to both leaflets after EM
> simulation. How to restrict PS just in one side?

Lipid flip-flop is not something that should occur during EM, or likely even 
during a short MD simulation.  Does grompp throw any warnings about mismatched 
names?  If it did, then your topology is out of order with respect to the 
coordinate file and grompp is assigning DPPS parameters to DSPC.  Given the 
differences between these lipids, though, I would think greater problems would 
arise, but I thought I'd throw that out there.

Is this a matter of lipids jumping across periodic boundaries?  You could always 
increase your box size along the membrane normal.

> Mention: If in 128 lipids membrane and the PS lipids are less than 35, PS
> lipids can stay in one leaflet of a membrane stably.

This statement makes it sound as if your system is simply unstable - higher 
concentrations of PS lipid shear apart and fly to the other leaflet because they 
were unstable.

> So Can you help me for this?

In this case, it would be extremely useful to post some images online - 
especially the starting configuration as well as the structure after EM, colored 
in some meaningful way to show the differences you're seeing.  Instructions for 
posting images can be found at the following link, under the fourth bullet:




Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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