Hi Daniel,
After looking through the system energies throughout my three simulations
there appears to be a a significant jump in energy which can be here ->
http://research.parkerdewaal.com/furge/pot_energy.xlsx
Additionally looking at the last frame of the previous simulation, the
density in, the ions appear to be normally scattered throughout the
periodic box. Confusing.
Hi Carlos,
the # NVE Equilibirum for 1 ns is where this jump is occurring, however
please note that this is a typo and should be NPT, not NVE. The
equil.infile can be found in the first email of this chain. Hope that
helps.
Best,
Parker
On Thu, Jul 11, 2013 at 8:45 AM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> which of the multiple md steps in this script has the problem?
> On Jul 10, 2013 8:24 PM, "Parker de Waal" <Parker.deWaal09.kzoo.edu>
> wrote:
>
> > Hi Carlos,
> >
> > My run script can be found here ->
> > https://gist.github.com/ParkerdeWaal/6729efb75c9e09d5829b
> >
> > Please let me know if this is not what you were looking for or if I can
> > provide additional details.
> >
> > Parker
> >
> >
> > On Wed, Jul 10, 2013 at 9:05 PM, Carlos Simmerling <
> > carlos.simmerling.gmail.com> wrote:
> >
> > > It's in the run script. Send that too...
> > > On Jul 10, 2013 7:57 PM, "Parker de Waal" <Parker.deWaal09.kzoo.edu>
> > > wrote:
> > >
> > > > 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 Thu Jul 11 2013 - 07:00:02 PDT
