Hi, As Justin had already suggested, restraints will lead to nasty atomic clashes. Looking at the gro file you have provided, it seems that the system is very poorly equilibrated.
I had a similar issue. If the forcefield you are using is accurate enough, follow the steps as follows: 1. Take the system and increase the box size in all the directions. Run energy minimization. This will give a somewhat better starting point for the membrane. 2. Now play around with the box size, such that the x-y dimensions conform to the reported APL value. Eg., suppose for POPC, you have 48 Lipids per leaflet and say the experimental APL is about 5.7 nm^2 then the x=y=sqrt(48*5.7) nm. Adjust the z direction according to what thickness of water you would want to have. 3. Solvate the system (using genbox maybe?). Albeit some water molecules will penetrate the lipids. Do not worry about that. If your forcefield is accurate enough, water molecules would diffuse to the top after you follow steps 4. 4. Position restraint the membrane and then use semi-isotropic pressure coupling but DO NOT position restraint water. Run NPT for maybe 4-5 ns. You would see that water has diffused to the top and that you have a very good initial condition. As I said, it all depends on the correctness of the forcefield that you are using, but I think any Lipid forcefield will be parameterized such that the tails would have hydrophobic characteristics and you would not have to worry about water penetrating the bilayer. -- View this message in context: http://gromacs.5086.x6.nabble.com/restraints-on-water-oxygen-atoms-tp5008823p5009030.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
