[gmx-users] high forces

francesco oteri francesco.oteri at gmail.com
Fri Jan 27 16:51:15 CET 2012

Dear gromacs users,
I  am attempting to simulate a protein with an active site containing to
metals (Ni and Fe). I am trying to mantain the active site structure
constraining bonds, angles and dihedrals.
When I simulate the active site alone in water, it remains stable. When I
insert the active site in the protein's scaffold, unfortunately,
the simulation crashes because of large vibration in bond lenght and angle
amplitude in the active site. I am not able to detect big clashes or any
structural distortion.

I tried to play with force constants, temperature, time-step, constrains,
etc.etc. but I am not able to mantain the simulation stability.

I am wondering whether exists a tool to dissect the energetic contributions
( including bonded parameters ) permitting me to identify the problem
giving rise the crash.

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