If you are running with a 2fs time step plus a thermostat and do not see
any explosions, expect to see one eventually. This is a highly unsafe
configuration and can appear to be under control until a few particles's
errant trajectories coincide and the energy spirals out of control. This
can happen in a few hundred steps after what is superficially normal
dynamics.
Dave
On Wed, Jun 26, 2019 at 5:09 PM Kenneth Huang <kennethneltharion.gmail.com>
wrote:
> Hi Dave,
>
> Ah, that’d explain it. Oddly, it seems to work fine in sander as is, even
> with a 2 fs timestep (not sure if it won’t blow up later, though). It’s
> still pretty glacial, but worth a try anyway.
>
> Best,
>
> Kenneth
>
>
> On Wed, Jun 26, 2019 at 4:16 PM David Cerutti <dscerutti.gmail.com> wrote:
>
> > Try your input with sander; this looks like it may be one of the few
> > features that has not yet made its way to pmemd. Not only is sander
> going
> > to be very slow for production MD, this apparenty requires ntf = ntc = 1,
> > which means no SHAKE, which means 1fs time steps. Yikes! I guess I need
> > to implement an r-RESPA / MTS scheme in pmemd.cuda that will tolerate
> > flexible bonds to hydrogen...
> >
> > Dave
> >
> >
> > On Wed, Jun 26, 2019 at 4:07 PM Kenneth Huang <
> kennethneltharion.gmail.com
> > >
> > wrote:
> >
> > > Hi all,
> > >
> > > A quick question- I remember the Nose-Hoover thermostat was implemented
> > in
> > > pmemd, but a test with my input at ntt=9 keeps throwing up an error
> > message
> > > of how ntt can only be 0,1,2, or 3. Is that actually the case, or did I
> > > miss something up in the input?
> > >
> > > &cntrl
> > > imin = 0,
> > > irest = 1,
> > > ntx = 7,
> > > ntxo= 2,
> > > barostat = 1,
> > > pres0 = 1.0,
> > > ntp = 1,
> > > taup = 2.0,
> > > cut = 9.0,
> > > ntr = 0,
> > > ntc = 1,
> > > ntf = 1,
> > > tempi = 300,
> > > temp0 = 300,
> > > ntt = 9,
> > > gamma_ln = 1,
> > > ig=-1,
> > > iwrap=1,
> > > nstlim = 500000, dt = 0.008,
> > > ntpr = 75000, ntwx = 2000, ntwr = 150000,
> > > /
> > >
> > >
> > > Best,
> > >
> > > Kenneth
> > >
> > > --
> > > Ask yourselves, all of you, what power would hell have if those
> > imprisoned
> > > here could not dream of heaven?
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Received on Wed Jun 26 2019 - 19:00:03 PDT
