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 - 13:30:02 PDT
