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 - 09:00:04 PDT
