# Re: [AMBER] First to Second Frame Position Jump

From: Parker de Waal <Parker.deWaal09.kzoo.edu>
Date: Thu, 11 Jul 2013 22:43:21 -0400

Hi everyone,

I re-ran the equilibrium simulation using nstlim=2000,dt=0.002, ntpr=10,
ntwx=10 to capture more frames between this weird shift. Apparently my
temperature is skyrocketing upwards, among other settings, to 700 K before
leveling out all in the time of 2 ps. Graphs of density and temp can be
found here -> research.parkerdewaal.com/furge/temp_density.xlsx

I don't quite know how to explain as the simulation order goes NPT -> NPT
extended with less positional constraints...

Here is all supporting data:
# Provide density NPT
ibrun pmemd.cuda.MPI -O -i density.in -o density.out -p protein.prmtop -c
heat.rst -r density.rst -x density.nc -ref min_all.rst

# Equilibirum for 2 ps writing every 10 frames NPT
ibrun pmemd.cuda.MPI -O -i equil.in -o equil.out -p protein.prmtop -c
density.rst -r equil.rst -x equil.nc -ref min_all.rst

density.in:
density equilibration
&cntrl
imin=0,irest=1,ntx=5,
nstlim=50000,dt=0.002,
ntc=2,ntf=2,
cut=9.0, ntb=2, ntp=1, taup=1.0,
ntpr=500, ntwx=500,
ntt=3, gamma_ln=2.0,
temp0=300.0,
restraint_wt=2.0,
ioutfm=1,
/

equil.in
equil
&cntrl
imin=0,irest=1,ntx=5,
nstlim=2000,dt=0.002,
ntc=2,ntf=2,
cut=9.0, ntb=2, ntp=1, taup=2.0,
ntpr=10, ntwx=10,
ntt=3, gamma_ln=2.0,
temp0=300.0,
restraint_wt=0.5,
ioutfm = 1,
/

The only changes are the taup and restraint_wt to my knowledge,

Thanks again everyone!

Best,
Parker

On Thu, Jul 11, 2013 at 12:04 PM, Parker de Waal
<Parker.deWaal09.kzoo.edu>wrote:

> 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
>> >> >> > > > > > _______________________________________________
>> >> >> > > > > > AMBER mailing list
>> >> >> > > > > > AMBER.ambermd.org
>> >> >> > > > > > http://lists.ambermd.org/mailman/listinfo/amber
>> >> >> > > > > >
>> >> >> > > > > _______________________________________________
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>> >> >> > > > >
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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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>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
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Received on Thu Jul 11 2013 - 20:00:02 PDT
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