Does the reference coordinate set exactly match the inpcrd?
On Jul 10, 2013 6:47 PM, "Parker de Waal" <Parker.deWaal09.kzoo.edu> wrote:
> 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 - 17:00:04 PDT
