On Thu, Apr 2, 2015 at 12:41 PM, Quynh Vo <ziczac_nq.yahoo.com> wrote:
> Hi, thank you for your help. Yes I noticed those huge numbers too and I
> can't really understand how or why!! I used wrapping for both heat and
> production. I used ntb = 2 during heating to get the right density and
> volume. And this error did not occur using pmemd.MPI, only with pmemd.cuda
> My input file:
> &cntrl imin = 0, ntx = 5, irest = 1, iwrap = 1, ig = -1, tol =
> 0.000001, ntb = 1, cut = 10, ntt = 3, ntc = 2, ntf = 2, tempi = 298.15,
> temp0 = 298.15, gamma_ln = 5.0, ntp = 0, pres0 = 1.0, taup = 2.00, nstlim
> = 2000000, nscm = 1000, dt = 0.001, ntpr = 20000, ntwx = 20000, ntwr =
> 200000, nmropt=1,
> / &wt type='DUMPFREQ', istep1=1000, / &wt
> type='END' /DISANG=rst.dist3.00DUMPAVE=dist_3.00.dat Best regards,
> Quynh Vo
>
​What version of pmemd.cuda are you using (it should say near the top).
You should make sure that all updates are applied. Also, is this
pmemd.cuda serial, or pmemd.cuda.MPI? And do most of the pmemd.cuda tests
pass?
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Apr 02 2015 - 10:30:04 PDT
