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
(801) 585-9119 (Fax)
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Received on Thu Jul 11 2013 - 08:00:03 PDT
