[gmx-users] How to calculate the potential energy of a molecule in a fixed conformation.

[xiao]

Dear Justin,


Thank you so much for your help!


Best wishes


Fugui








At 2013-07-28 03:52:47,"Justin Lemkul" <jalemkul at vt.edu> wrote:
>
>
>On 7/27/13 11:48 AM, xiao wrote:
>> Dear Gromacs users,
>>
>> I am developing the force field parameters of an organic molecule. I need to calculate the MM energy of the molecule in a fixed conformation. For example, in order to get the force constant of a bond, i need to calculate the energy of the bond in different distance by using MM method and the QM method. Firstly, i plan to scan the bond of interest up to 0.1 angstrom from the equilibrium value at a step size of 0.005 angstrom while optimizing the structure at each step by using QM method. Secondly, i calculate the potential energy of each structure obtained in the previous QM optimizaiton step. Thirdly, i will calculate the energy difference between QM and MM calculation, and finally fit the force constant of the bond using the energy difference between QM and MM energy.   My question is that how i calculate the potential energy of each structure obtained in QM step? I think i can get an potential energy in energy minization step by using grompp method, but i am not sure whe
 !
> the
>>   r it is the energy i needed. Any advice is appreciated.
>>
>
>http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy
>
>-Justin
>
>-- 
>==================================================
>
>Justin A. Lemkul, Ph.D.
>Postdoctoral Fellow
>
>Department of Pharmaceutical Sciences
>School of Pharmacy
>Health Sciences Facility II, Room 601
>University of Maryland, Baltimore
>20 Penn St.
>Baltimore, MD 21201
>
>jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>
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