AMBER Archive (2005)

Subject: AMBER: GB with Langevin dynamics problem

From: Peter Varnai (pv232_at_cam.ac.uk)
Date: Tue Apr 05 2005 - 11:04:15 CDT

Dear Amber users,

I analyse a 50 ns long trajectory of a nucleic acid calculated by GB and
Langevin dynamics (amber 8). I noticed that at regular intervals the rms
and energy components had peaks:
http://cus.cam.ac.uk/~pv232/amber/amber.html

I used the following input:
 &cntrl
    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

I noticed that in the first 4 ns the peaks are more frequent which
coincides with the fact that here I used nstlim=100000. That would mean
that the restart of my trajectory fragments are not correct, but I am not
sure why. Any suggestion what might have gone wrong would be appreciated.

Thanks,
Peter
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