HI Dan,
Frames 0-50 are heating (2 fs step size, writing every 1 ps (or 500 steps) )
51-100 are density in (same as above)
102-1100 is the equilibrium simulation (1 ns in length with a writing every
2 ps or 1000 steps)
This is a quick reason why there is no frame 101.
Parker
On Thu, Jul 11, 2013 at 11:41 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Why is there no data for frame 101? Something must have changed in the
> coordinates from frame 100 to frame 102 for the system to go from a
> density of 1.0195 to 0.9813.
>
> -Dan
>
> On Thu, Jul 11, 2013 at 9:31 AM, Parker de Waal
> <Parker.deWaal09.kzoo.edu> wrote:
> > 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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> >> >> > > > > >
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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
> >> (801) 585-9119 (Fax)
> >>
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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
> (801) 585-9119 (Fax)
>
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Received on Thu Jul 11 2013 - 09:30:03 PDT
