[AMBER] First to Second Frame Position Jump

From: Parker de Waal <Parker.deWaal09.kzoo.edu>
Date: Wed, 10 Jul 2013 19:45:15 -0400

Hi Everyone,

I've come across an issue where between the first and second frame of an 1
ns equilibrium simulation (NPT ensemble, position restrained, post heating
and density additions) my protein and ions seem to jump drastically causing
a very large rmsd. Additionally it seems that my ions are clumped together
on the first frame and re-enter the solution during the second frame.

Here are my simulation parameters:
  cut=9.0, ntb=2, ntp=1, taup=2.0,
  ntpr=1000, ntwx=1000,
  ntt=3, gamma_ln=2.0,
  ntr=1, restraintmask=':1-466',
  ioutfm = 1,

Maybe irest should equal 0? Or maybe I need to supply a tempi?

For those interested I have uploaded the first 20 frames of simulation,
sans water, here -> research.parkerdewaal.com/furge/prot_traj.zip

Thanks Everyone again!

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Received on Wed Jul 10 2013 - 17:00:03 PDT
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