After all this discussion regarding graphite, I have a related question:
Is sander able to simulate covalently bonded periodic infinite crystals?
I worry that sander will get confused whenever a covalent bond crosses
the periodic boundary.
I suspect this topic has come up before. If so, forgive me.
(I'm under the impression that in Bongkeun's graphite example,
"bondbydistance" was occasionally inserting bonds between atoms on
opposite sides of the unit cell, and that is is why the system
appeared to be curving in on itself during equilibration. Stability
appeared to be restored when these bonds were cut. However I imagine
that we might want to include bonds for the boundary atoms. It's not
hard to add these additional bonds manually using the "bond" command
in leap, but I suspect that sander will misinterpret them.)
Similar issues also come up when simulating infinite helices or long
cellulose chains.
Thank you
Andrew
This email is related to earlier posts titled:
"Problem using graphite structure in equil MD"
On Thu, Oct 21, 2010 at 4:31 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>> In sum up, larger structure can avoid making wrong bonds in leap.
>> I guess there is threshold value to make a bond in the inside of leap.
>
> It looks like bondbydistance 1.5 worked after all.
> Excellent!
> Bill
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Received on Thu Oct 21 2010 - 18:00:03 PDT
