Hi,
It looks like your graphite layer is not stable. I think either your
initial structure or your model is wrong.
See what happens if you change the dumpout frequency (ntwx=1).
I am not an expert on graphite but carbons of graphite has no charge? It
sound odd to me.
On Wed, Oct 20, 2010 at 1:24 AM, Bongkeun Kim <bkim.chem.ucsb.edu> wrote:
> Hello,
>
> I made a parameter file for a graphite layer with two carbons based on the
> crystal unit cell.
> An I generate a big monolayer of graphite using the matrix information of
> the unit cell.
>
> Using the following input file, I was able to minimize this graphite which
> is solvated by TIP3P waters.
> ==============================================
> graphite-water min 1
> &cntrl
> imin = 1,
> maxcyc = 1000,
> ncyc = 500,
> ntb = 1,
> ntr = 1,
> cut = 10.0
> /
> Hold the graphite fixed
> 5000.0
> RES 1 120
> END
> END
> ==============================================
>
> But in the heat and equilibrium stage, the segmentation fault occurs with
> sander and pmemd and it only gives a NaN output with pmemd.cuda.
> The input file of heating is this:
> =========================================
> &cntrl
> imin = 0,
> irest = 0,
> ntx = 1,
> ntb = 1,
> cut = 10.0,
> ntr = 1,
> ntc = 2,
> ntf = 2,
> tempi = 0.0,
> temp0 = 300.0,
> ntt = 3,
> gamma_ln = 1.0,
> nstlim = 10000, dt = 0.002
> ntpr = 50, ntwx = 100, ntwr = 1000
> /
> Hold the graphite fixed
> 10.0
> RES 1 120
> END
> END
> =================================================
>
> I'll send all the output files.
> If you have any idea to deal with the graphite molecules(periodic bonded),
> please let me know.
> Thank you.
> Bongkeun Kim
>
>
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>
--
Best,
InSuk Joung
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Received on Wed Oct 20 2010 - 10:00:05 PDT
