On Mon, Sep 09, 2019, Parviz Seifpanahi Shabane wrote:
>I am running the implicit solvent simulation, everything works without any
>error until the "production" step. The simulation stops at production
>without giving any error message!!!
>======================================================================
>This my "production" input file:
>======================================================================
>Hexosome md
> &cntrl
> imin = 0, irest=1, ntx=5, ig=-1,
> ntc=2, ntf=2,
> igb = 5, gbsa = 0,
> ntpr = 1000, ntwx = 1000, ntwr=1000,
> ntt = 3, gamma_ln = 0.01,
> temp0 = 380.0,
> nstlim = 14000000, dt = 0.002,
> cut = 9999.0, ntb = 0,
>saltcon = 1.0,
> ntr=1,
>restraint_wt=10.0,
>restraintmask=':1-294,333-429,449-531,552-642,684-782,818-916,940-1018,1037-1133,1172-1268'
> /
>END
Try a run with ntpr=1, nstlim=100, to see if that gives any extra info.
Also, double check the differences between the mdin files for the
equilibration and production steps that might cause problems. Are you
able to extend the equilibration phase (just as a check, do a short
run)? Finally, double/triple check the file names you are using when
you call pmemd.
....dac
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Received on Tue Sep 10 2019 - 06:00:03 PDT
