[gmx-users] bad contacts on lipid tails

[Mohsen Ramezanpour]

Dear Gromacs users,

I am doing simulations in HII phase in absence of any sugar or alkane to
fill the gaps (in other words, HII in water)
In few of my systems (which I made), there are lipids which their tails
have bad contacts. Based on visualization, the CH2-CH2 bond from one tail
in lipid 1 cross the CH2-CH2 bond in the tail from an adjacent lipid. They
kinda stuck there.

Interestingly, these systems are running properly during EM step, as well
as MD with a time step of 1 fs but fail with 2 fs, even after 45 ns of
simulation with 1 fs. The lipid-lipid contacts cause LINCS errors for
angles on those bonds and involved hydrogens, and eventually, the system
will blow up.

This is what I understand after many tests to figure out the problem for
this failure (segmentation fault (core dumped)). The topology of the
molecule is correct and there is not water molecule which causes the
problem. I also did simulations on one lipid both in the vacuum and in
water. Everything is fine. The system setup is the only thing which I am
suspicious about.

Is there any trick to:

1) recognize these bad contacts? (I deleted few lipids but still, there are
other lipids which cause the problem)

2) remove these bad contacts? (applying stronger bond and angle force
constant, changing the LINCS parameters, or something like these?)

I highly appreciate your help in advance,
Cheers
Mohsen

-- 
*Rewards work better than punishment ...*