Re: AMBER: GB with Langevin dynamics problem

From: Andreas Svrcek-Seiler <svrci.tbi.univie.ac.at>
Date: Tue, 5 Apr 2005 19:04:08 +0200 (CEST)

Hi,
> 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 can't see anything suspicious here at first glance (being not too
familiar with all options), but
your signal (e.g. from rms-2.jpeg) shows signs of (quasi-)periodicity.
(ten "big spike" intervals between tic 400 and tic 500 in whatever units).
Comparing the inter-spike intervals with your input *might* give a clue.

I hope that helps,
good luck
Andreas 

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Received on Tue Apr 05 2005 - 18:53:00 PDT
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