Hi Dai,
Please don't e-mail me directly. It gets lost in my e-mail box and prevents
others from answering your question (or seeing my reply).
As I believe I note in the source code, these discussions are from the Towhee
webpages:
http://towhee.sourceforge.net/forcefields/uff.html
I don't believe the general case is to be adjusted.
-Geoff
> On May 14, 2018, at 6:22 PM, Tang, Dai <dai.t...@chbe.gatech.edu> wrote:
>
> Hi Geoff,
>
> One more question related:
> In src/forcefielduff.cpp, it mentioned that there was a fixed typo from Rappe
> paper, so that case 1 of VectorAngleDerivative gives:
> energy = ka * (1.0 + cos(theta))
>
> I don't know if the energy of case 6 should also be fixed or not.
> energy = ka * (1 - cos(n*theta)) + exp(-20.0*(theta - theta0 + 0.25))
>
>
> Thank you.
>
> Dai
>
> From: Geoffrey Hutchison <geoff.hutchi...@gmail.com>
> Sent: Tuesday, May 8, 2018 3:41:32 PM
> To: Tang, Dai
> Cc: openbabel-disc...@lists.sf.net
> Subject: Re: [Open Babel] print UFF parameters
>
>> Is there a way to print the UFF parameters for each molecule in database, or
>> even potential formula of each term such as valence, bonded or non-bonded,
>> so that I can use them for other MD / MC engines?
>
>
> Right now, you'd need to edit the source, e.g., src/forcefields/*uff.cpp
>
> By default, you can get a number of the components with verbose logging of
> the forcefield code, e.g.
>
> % obenergy -ff UFF c60.xyz <http://c60.xyz/>
>> A T O M T Y P E S
>>
>> IDX
>> TYPE RING
>> 1 C_R AR
> ...
>> 60 C_R
>> AR
>>
>> S E T T I N G U P C A L C U L A T I O N S
>>
>> SETTING UP BOND CALCULATIONS...
>> SETTING UP ANGLE CALCULATIONS...
>> SETTING UP TORSION CALCULATIONS...
>> SETTING UP OOP CALCULATIONS...
>> SETTING UP VAN DER WAALS CALCULATIONS...
>>
>> E N E R G Y
>>
>> TOTAL BOND STRETCHING ENERGY = 816.180 kJ/mol
>> TOTAL ANGLE BENDING ENERGY = 1214.059 kJ/mol
>> TOTAL TORSIONAL ENERGY = 7998.311 kJ/mol
>> TOTAL VAN DER WAALS ENERGY = 471.619 kJ/mol
>>
>> TOTAL ENERGY = 10759.59508 kJ/mol
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