[gmx-users] Calculation of the Force on the center of bonds

[Rasoul Nasiri]

Dear Erik,

Many thanks for your comment.

The situation seems to be similar to TIP4P water model where the M
site is located among the three other atoms. In my case, it's between
the two C-H atoms.

Could I ask you which parameters must be selected for these virtual sites?

The interest molecule is n-alkane that have (2n+2) C-H bond. Is that
make sense that I put the virtual sites there?

Best
Rasoul

On Mon, Feb 11, 2013 at 5:33 PM, Erik Marklund <erikm at xray.bmc.uu.se> wrote:
> Try virtual sites constructions.
>
>
> On Feb 11, 2013, at 6:01 PM, Rasoul Nasiri wrote:
>
>> Dear All,
>>
>> I need to define interaction sites on the center of C-H bonds instead
>> of nuclei of each atom. The main reason was that non-bonding
>> parameters (sigma and epsilon) have been parametrized in these centers
>> and those are only available for the center of C-H.
>>
>>
>> So, I just wanted to know how calculation of force can be implemented
>> by GROMACS in this case.
>>
>>
>>
>> Best wishes
>> Rasoul
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