RATTLE Error During Minimization of Charmm Gui Generated Bilayer

From: begüm alaybeyoğlu (bgmalay_at_gmail.com)
Date: Tue Dec 15 2015 - 10:27:48 CST

Dear NAMD users,

I am having trouble with the Charmm Gui generated POPE bilayer. After
having run all the minimization-equilibration-production steps, I ran a 25
ns production simulation (step.7.1) without any problems. What I wanted to
do was to get the last snapshot of my equilibrated bilayer, place my
peptide on top of it, autoionize the system and run a quick minimization &
equilibration before I start the peptide translocation simulation.

Now I keep getting the RATTLE error (for atoms of bilayer always) just
after the minimization is completed and I tried all of the previously
suggested solutions, such as decreasing the timestep or nonbondedFreq or
fullElectFrequency or stepspercycle and increasing the minimization steps
etc. When I plotted the energy I saw that around 2500 steps of minimization
was enough already. I tried slow heating of the system, but the error did
not change. By decreasing my dcdfreq to 10 steps, I observed that H atoms
(bound to C or N) actually start to overlap during the minimization, so the
cause of the error is probably this.

I have run many similar simulations with charmm27 before without any
problems.This is the first time I built the whole system from scratch using
the charmm36 parameters, so I am not sure what is going on. Any suggestions
are welcome.


Begum Alaybeyoglu

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