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:
Equil
&cntrl
imin=0,irest=1,ntx=5,
nstlim=500000,dt=0.002,
ntc=2,ntf=2,
cut=9.0, ntb=2, ntp=1, taup=2.0,
ntpr=1000, ntwx=1000,
ntt=3, gamma_ln=2.0,
temp0=300.0,
ntr=1, restraintmask=':1-466',
restraint_wt=0.5,
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!
Parker
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Received on Wed Jul 10 2013 - 17:00:03 PDT
