[gmx-users] Error during CNP simulation

Christopher Neale chris.neale at mail.utoronto.ca
Tue Oct 30 01:47:57 CET 2012

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?


-- 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

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.


More information about the gromacs.org_gmx-users mailing list