Hi Hoshin,
AMBER and leap were not really designed with the system you want in mind. I
think you need to examine how exactly that force field is supposed to work
and make sure it is compatible with the AMBER force field form.
Specifically, the 1-4 non-bonded interaction scaling in AMBER may not be
what you want.
As for bondByDistance, it seems that a judicious choice of the cutoff
length should give the behavior you want, depending on the atom packing.
Regards,
Brain
On Fri, Oct 25, 2013 at 11:39 AM, Hoshin Kim <85hskim.gmail.com> wrote:
> 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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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
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Brian Radak : BioMaPS
Institute for Quantitative Biology
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Received on Fri Oct 25 2013 - 11:30:04 PDT
