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

From: Parker de Waal <Parker.deWaal09.kzoo.edu>
Date: Fri, 12 Jul 2013 13:02:50 -0400

I believe I've found the source of this energy change, however I do not
know how to fix the problem.

Upon inspecting both the density.out and equil.out I noticed that the the
box seems to be changing size (which would account for the change in
pressure/temp/volume/etc)

Taken from density.out:
| Coordinate Index Table dimensions: 18 16 17
| Direct force subcell size = 5.1619 5.0825 5.1869

Taken from equil.out:
| Coordinate Index Table dimensions: 17 15 16
| Direct force subcell size = 5.1236 5.0821 5.1663

Has anyone encountered this before? Consider that both of these two
simulations are NPT I would assume that the box would remain constant
between them.

Best,
Parker

On Thu, Jul 11, 2013 at 10:43 PM, Parker de Waal
<Parker.deWaal09.kzoo.edu>wrote:

> 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
>>> >> >> > > > > >
>>> >> >> > > > > _______________________________________________
>>> >> >> > > > > AMBER mailing list
>>> >> >> > > > > AMBER.ambermd.org
>>> >> >> > > > > http://lists.ambermd.org/mailman/listinfo/amber
>>> >> >> > > > >
>>> >> >> > > > _______________________________________________
>>> >> >> > > > AMBER mailing list
>>> >> >> > > > AMBER.ambermd.org
>>> >> >> > > > http://lists.ambermd.org/mailman/listinfo/amber
>>> >> >> > > >
>>> >> >> > > _______________________________________________
>>> >> >> > > AMBER mailing list
>>> >> >> > > AMBER.ambermd.org
>>> >> >> > > http://lists.ambermd.org/mailman/listinfo/amber
>>> >> >> > >
>>> >> >> > _______________________________________________
>>> >> >> > AMBER mailing list
>>> >> >> > AMBER.ambermd.org
>>> >> >> > http://lists.ambermd.org/mailman/listinfo/amber
>>> >> >> >
>>> >> >> _______________________________________________
>>> >> >> AMBER mailing list
>>> >> >> AMBER.ambermd.org
>>> >> >> http://lists.ambermd.org/mailman/listinfo/amber
>>> >> >>
>>> >> > _______________________________________________
>>> >> > AMBER mailing list
>>> >> > AMBER.ambermd.org
>>> >> > http://lists.ambermd.org/mailman/listinfo/amber
>>> >>
>>> >>
>>> >>
>>> >> --
>>> >> -------------------------
>>> >> 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)
>>> >>
>>> >> _______________________________________________
>>> >> AMBER mailing list
>>> >> AMBER.ambermd.org
>>> >> http://lists.ambermd.org/mailman/listinfo/amber
>>> >>
>>> > _______________________________________________
>>> > AMBER mailing list
>>> > AMBER.ambermd.org
>>> > http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>>
>>>
>>> --
>>> -------------------------
>>> 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)
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jul 12 2013 - 10:30:02 PDT
Custom Search