Dear Amber specialists,
I have created (100) Au surface, and also got the non bonded energy (NONB)
term of Au in frcmod. But When I performed simulation, All Au atoms
composed of surface fell apart.
So, I am going to use "bondbydistance" command in xleap in order to hold
each Au atom. However, since that command makes so many covalent bonds like
spiders web, simulation became slow, and moreover, I am worried whether or
not that surface is correct in terms of bonds (usually Au is bonded each
other as metallic or secondary bonds).
I would appreciate it a lot if you ,
1) tell me whehter or not using bondbydistance command makes sense
2) give any good idea for making surface
3) check and mention incorrect part of frcmod file attached below.
=============frcmod for Au ==============
remark goes here
MASS
Au 196.967
BOND
s-Au 37.87 2.650 Cummings recalculated from Morse
Au-Au 303.84 2.88
ANGLE
c3-s-Au 11.600 99.500 R. Henda, AlChE Journal 46(2000)1275
Au-Au-s 0.0 90.0
Au-Au-Au 0.0 0.0
DIHE
O2-c3-s-Au 0.0 0.0
h1-c3-s-Au 1 0.0 0.0 2.000
Au-Au-Au-s 0.0 0.0
Au-Au-s-c3 0.0 0.0
Au-Au-Au-Au 0.0 0.0
s-Au-Au-s 0.0 0.0
c3-c3-s-Au 1 0.0 180.0 2.000
IMPROPER
NONB
Au 1.467 0.039
====================================
Thanks in advance,
Hoshin
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Received on Fri Oct 25 2013 - 09:00:02 PDT
