Hi Carlos,
To my knowledge the initial protein.prmtop matches the protein.inpcrd,
however I don't know how to check this. Do you have any suggestions?
Best,
Parker
On Jul 10, 2013 7:51 PM, "Carlos Simmerling" <carlos.simmerling.gmail.com>
wrote:
> 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 - 18:00:02 PDT
