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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Received on Tue Oct 19 2010 - 22:30:04 PDT
