Hi Daniel,
upon first glance my system does seem to have reached a density equilibrium
before the 1 ns equil simulation is run. Please see attached density plot
->
http://research.parkerdewaal.com/furge/density.xlsx
I'll re-run the equil simulation for 1000 steps, writing every 10, and
report back soon.
Best,
Parker
On Thu, Jul 11, 2013 at 10:44 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> It's still not clear to me that you actually have a problem. The
> energy in the plot you attached does increase a bit at step 102 but
> then looks like it settles down and is nice and steady. Does your
> density appear to be equilibrating? If your previous simulation was
> done with constant volume but the density was not properly
> equilibrated you could see such a jump upon switching to constant
> pressure.
>
> If you really want to see what's going on with your system around the
> time of the energy jump you should restart it and run for 1000 steps
> only, but write your trajectory and output every 10 steps (or even
> every single step).
>
> -Dan
>
> On Thu, Jul 11, 2013 at 7:36 AM, Parker de Waal
> <Parker.deWaal09.kzoo.edu> wrote:
> > 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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>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
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Received on Thu Jul 11 2013 - 09:00:03 PDT
