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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Received on Thu Jul 11 2013 - 06:00:02 PDT
