> I tried to make bigger graphite about 200 atoms.
> I just found that UCSF chimera can make this structure from the unit
> cell pdb(2c.pdb) file by supercell operation and it can also generate
> proper bonds between carbons and finally I can see a good graphite
> with all 6-membered rings(c10-1.pdb).
>
> I loaded this pdb with previous generated prepi file from 2-carbon
> unit cell(2c.prepi).
> --------------------------------------------------
> source leaprc.ff99SB
> source leaprc.gaff
> loadamberprep c2.prepi
> gr=loadpdb c10-1.pdb
> savepdb gr c10amb.pdb
> solvatebox gr TIP3PBOX {0 0 20}
> saveamberparm gr c10.prmtop c10.inpcrd
> ---------------------------------------------------
> After loading prmtop and inpcrd files, I see additional bonds between
> two edge carbons. And after minimization with waters, I see tube like
> structure instead of flat surface. I think leap generate wrong bonds.
The most reliable way to see if leap adds any bonds is to look
in xleap ("edit gr"). Also VMD should show this if you load
prmtop.
> ======================================
> sam wat heat 1
> &cntrl
> imin = 0,
> irest = 0,
> ntx = 1,
> ntb = 1,
> cut = 10.0,
> ntr = 1,
> ntc = 2,
> ntf = 2,
> tempi = 0.0,
> temp0 = 50.0,
> ntt = 3,
> gamma_ln = 1.0,
> nstlim = 10000, dt = 0.0005
> ntpr = 50, ntwx = 100, ntwr = 1000
> /
> Hold the SAM fixed
> 50.0
> RES 1 100
> END
> END
> ===================================
> And with the slow heating from 0 to 50K, I see NaN error again.
> Could you give me any idea how to solve all these problem?
That's fast heating to 50K, but such a low temp should be ok.
(For slow heating, one would use a graduated temp restraint.)
How many steps before the NaN error? I would set ntwx=1 to dump
coordinates for every frame, then watch the movie (e.g. in VMD)
and see what is happening.
Bill
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Received on Thu Oct 21 2010 - 10:30:04 PDT
