Thanks George,
I tried your suggestion and saw considerable improvement on the GPUs. So, over the weekend I tried a few variations. FWIW, smaller values of SHAKE tolerance had worse energy conservation. Fortunately, I was able to get acceptable energy conservation with
cut=9
dsum_tol=1e-7
dt=0.0005
Heating is about 0.1 K over 50 ns, at least for this test system.
Thanks,
Tyler
> On Apr 4, 2017, at 4:36 PM, George M Giambasu <giambasu.gmail.com> wrote:
>
> Give this a try - it worked for me with both cpu & gpu versions of pmemd
> with NVE simulations. Increasing the shake tolerance can help with
> energy conservation.
>
>
> MD NVE
> &cntrl
> imin = 0, irest = 1, ntx = 7,
> cut = 9.0,
> ntc = 2, ntf = 2, tol = 0.0000005
> nstlim = 7500000, dt = 0.001,
> ntt = 0, ntb = 0, ntb =1 ,
> ntpr = 2000,
> ntwx = 2000,
> ntwr = 2000,
> ioutfm = 1,
> iwrap = 1
> /
> &ewald
> dsum_tol = 0.000001
> /
>
> -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Dr. George M. Giambasu
> Rutgers, The State University of New Jersey
> 174 Frelinghuysen Road, Room 308E Piscataway,
> NJ 08854, USA giambasu.rutgers.edu
> www.rci.rutgers.edu/~giambasu
> Office: 1-848-445-5223 Cell: 1-612-644-8285
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
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Received on Mon Apr 10 2017 - 14:00:02 PDT
