Sorry Bharath, I simply can not believe that a macromolecule drifted 3 nm during energy minimization. What happened to the intervening solvent? I think that you have some problem with your technique here.
Why did you use 120 constraints? Is this for bonds within the CNP? You need to do 2 things: a) figure out what is going wrong with your EM... what you describe seems impossible to me. b) simplify your system to debug the problem. So you get the same warnings about too many constraints if you omit the position restraints? Chris. -- original message -- You're right, my resizing from 7.5 nm to 15 nm refers to the dimension normal to the lipid bilayer (in this case, the x dimension) My bilayer center of mass is at around +3 nm, and I placed the CNP at around 10 nm to start with. I had periodic boundary conditions employed in all three dimensions. I didn't add the CNP using genbox or any other command- I manually manipulated the .gro coordinate file of the bilayer. When I ran an energy minimization of just the bilayer and the CNP, the nanoparticle moved, but very slightly- so far, so good. But, once I added water and did another energy minimization and checked the structure after convergence, the nanoparticle had drifted all the way up to around 0 nm, which meant it was only around 1 nm away from my bilayer before the MD run. So, yes, it drifted during the energy minimization. I should probably try what you said. I repeated the entire above process using a posre.itp file. I had created this posre.itp file using the the lipids in the bilayer, and the CNP atoms, and I used this file during the energy minimization after adding water, which is when i got the following error- "A charge group moved too far between two domain decomposition steps.". I also got a warning before the fatal EM, which said that the number of constraints I had imposed on the CNP (120) is greater than the number of possible degrees of freedom (48), which could cause the system to be unstable. I wasn't sure how to fix that, though. I'm sorry if I'm a bit vague, but I'd appreciate if you could advice me more on this issue. Thanks! Bharath -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
