Dr. Case,
Thanks for your quick reply. I knew that Amber was not coded for
bonding interactions with PBC but I do need to do that with network
solid involved. The VDW and electrostatic interactions are fine in my
simulation. I only need to calculation the bond lengths, bond angles
and dihedral angles with PBC. Could you please help me to do that?
Appreciations.
With regards,
Yubo
On Tue, 16 Feb 2010 07:34:33 -0500
case <case.biomaps.rutgers.edu> wrote:
> On Tue, Feb 16, 2010, Yubo Fan wrote:
>>
>> I'm trying to do some simulations with PBC for bonding interactions.
>> For example, graphite. The carbon atoms connecting from one end to
>>the
>> other should have covalent bonds. But the Amber seems not to compute
>> the bond energy using PBC. The calculations failed with
>>exceptionally
>> long bond lengths. I'm trying to modify the pmemd code by passing
>> pbc_box information into bonds.fpp, angles.fpp and dihedrals.fpp but
>> did not figure out how. Any advise? Thanks in advance.
>
> Amber is not coded for periodic simulations in which there are
>covalent bonds
> across unit cells.
>
> ....dac
>
>
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Yubo Fan
Chemistry Department
Texas A & M University
Tel: (979) 845-5237
Email: yubofan.mail.chem.tamu.edu
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Received on Tue Feb 16 2010 - 10:30:03 PST
