AMBER Archive (2004)

Subject: AMBER: A few questions in the protein unfolding simulations using GB model

From: Jiayun Pang (
Date: Tue Jan 27 2004 - 14:33:15 CST

Dear Amber Users,

I am trying to use the GB implicit solvent model to simulate the unfolding of a dimeric protein at elevated temperatures, for instance, 500 K and 600 K.


My input file is:



    ntx=5, irest=1,


    cut=16.0, igb=1, gbsa=1,

    ntt=1, tempi=600.0, temp0=600.0, tautp=2.0

    ntf=2, ntc=2, tol=0.000001,

    ntpr=100, ntwx=1000,

    nstlim=500000, dt=0.002,



RES 1 328




It took 2.5 days to run a 1 ns simulations to the monomeric structure (164 residues) while it took 12 days to finish a 1 ns run on the dimeric structure. This time difference, I think, is a bit surprising.


And also, when I visualized the trajectory files, I found the two subunits of the dimer began to separate (which is as what I expected) but were almost 300 Å away from each other within 1 ns at 600K, and therefore the αC rmsds reached around 200 Å. It is bizarre as I assume such thing won’t happen in the simulation using an explicit solvent model with PBC applied. Is there any way to judge a GB model simulation?


I am thinking of doing the simulations using explicit solvent model as a comparison. In Valerie Daggett’s unfolding papers, the water density was set to the experimental values at certain temperatures. I am wondering whether it could be done in Amber7 as well. And also, when I did simulations using the TIP3P water box at room temperature (300 K), the water density couldn’t reach the experimental water density value (0.997 gm/ml), no matter how long the constant pressure equilibration I did (hundreds of pico seconds).


Quite a few questions here. Thanks a lot in advance for any answer.



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