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 - 14:30:03 PDT
