AMBER: GB with Langevin dynamics problem 2

From: Peter Varnai <>
Date: Fri, 8 Apr 2005 17:29:08 +0100 (BST)

Dear Amber users,

I continue to look into the problem of quasi-periodic behaviour in
Langevin simulations in Amber8. I created a small system to test different
input parameters and I could reproduce the following behaviour in a
consistent manner. I used the following input:

    ntx=5, ntpr=500, ntwr=500, ntwx=500, ntwe=500,
    nstlim=500000, nscm=1000, ntf=2, ntc=2, ntb=0, ntp=0,
    irest=1, ntt=3, temp0=300, gamma_ln=5, cut=99.0, rgbmax=99, dt=0.002,
    ntr=0, saltcon=0.1, gbsa=1, surften=0.005, igb=1 &end

The result shows constant and large translational movement of the
molecule. This was checked visually and by non-fitted rmsd along the
merged trajectory. Apparently, the removal of trans/rot at default 2 ps
cannot cope with it. The "KE Trans" values reported in the outputs are
identical (eg: between run1.out run10.out), but the "KE Rot" shows
quasi-periodic behaviour along trajectory too. This effect is clearly
related to the restarting frequency of the simulation. Although increasing
the trans/rot removal frequency to 2 fs (every step) stops the overall
translation (so it works!), the molecule experiences small but identical
COM trans/rot energies between different fragments of the trajectory.
Quasi-periodicity is also seen in E_kin or rmsd values along the
trajectory. That the problem is truly related to Langevin was checked by
setting gamma_ln=0 and no problem was observed.

Therefore, it seems to me that something is either wrong with the
writing/reading of the restart file and/or each time sander restarts it
assigns some constant, non-random forces to the system?!

Before looking into the code, I wonder if someone has other idea what is
wrong? If anyone needs I can send a test case or the analysis results
described above. Lastly, has anyone carried out long and reasonable
Langevin simulation with Amber 8?

Peter Varnai
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Received on Fri Apr 08 2005 - 17:53:00 PDT
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