Dear Amber community,
Thanks for all your previous help. I want to restate my problem
more clearly.
For states V0 and V1 unperturbed atoms (in other words, the same atoms
with the same coordinates), do they need to have exactly the same charges?
It seems that for V0 ->V1, V1 may copy the charges from V0 and for V1->V0,
V0 may copy the charges from V1. This may lead to the wrong Hamiltonian.
I guess I need to make the unperturbed atoms have exactly the
same charges. The way to do this is to change the charges of the perturbed
atoms to make the formal charges the same.
Could anyone give me some comments over this issue? Many thanks
in advance.
Yulin
On Sat, Dec 8, 2012 at 10:13 PM, Yulin Huang <yulinhuang2007.gmail.com>wrote:
> Hi, Professor David Case. Thank you so much for your reply.
>
> Yulin
>
>
> On Sat, Dec 8, 2012 at 10:03 PM, case <case.biomaps.rutgers.edu> wrote:
>
>> On Sat, Dec 08, 2012, Yulin Huang wrote:
>>
>> > For thermodynamic integration, do corresponding same atoms in
>> > ligand pairs need to have the same charge?
>>
>> No. For most changes of interest, corresponding atoms in V0 and V1 would
>> in
>> fact *not* have the same charge.
>>
>> > It seems that it may affect the energy calculation.
>>
>> Indeed.
>>
>> ...good luck...dac
>>
>>
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>
>
>
> --
> Yulin "Joyce" Huang
> Ph.D Candidate
> Computational Chemistry (CADD)
> Advisor: Dr. Robert C. Rizzo
> State University of New York at Stony Brook
> Stony Brook NY,11790
> Office: (631)632-8519
>
--
Yulin "Joyce" Huang
Ph.D Candidate
Computational Chemistry (CADD)
Advisor: Dr. Robert C. Rizzo
State University of New York at Stony Brook
Stony Brook NY,11790
Office: (631)632-8519
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Received on Mon Dec 10 2012 - 10:00:03 PST
