[gmx-developers] Contribution of inter-molecular distance restraints to the virial

[Alexander Kuhn]

Hi,

we understand it so far.
But are distance restraints considered as
'normal' bonded interactions in this respect?
We can't find it in calcvir.c.

Cheers,
Alex


> Hi,
> 
> For all normal bonded and non-bonded interactions the virial
> contribution is determined "automatically" in calc_virial. This is done
> using a single sum and so called shift forces (see manual).
> The COM pull force is special and is added after calc_virial and the
> virial contribution is (has to be) calculated separately.
> 
> Cheers,
> 
> Berk
> 

On 05/05/2015 09:32 AM, Alexander Kuhn wrote:
>> Hi,
>> we use half-harmonic distance restraints between COM of a solute and a
>> number of waters around it.
>> Does Gromacs (gromacs-4.6.3) account for the contribution of these
>> inter-molecular distance restraints to the virial?
>> 
>> 
>> Where can it be found/included in the code? In disre.c ?
>> 
>> We found the virial contribution to the pull code in pull.c:
>> 
>> if (vir && bMaster) {
>>             /* Add the pull contribution to the virial */
>>             for(j=0; j<DIM; j++)
>>             {
>>                 for(m=0; m<DIM; m++)
>>                 {
>>                     vir[j][m] -= 0.5*f[j]*r_ij[g][m];
>>                 }
>>             }
>> Can it be done in a similar way for the distance restraints?
>> 
>> Thanks, Alex
>> 
>> 


On 2015-05-05 09:32, Alexander Kuhn wrote:
> Hi,
> we use half-harmonic distance restraints between COM of a solute and a
> number of waters around it.
> Does Gromacs (gromacs-4.6.3) account for the contribution of these
> inter-molecular distance restraints to the virial?
> 
> 
> Where can it be found/included in the code? In disre.c ?
> 
> We found the virial contribution to the pull code in pull.c:
> 
> if (vir && bMaster) {
>             /* Add the pull contribution to the virial */
>             for(j=0; j<DIM; j++)
>             {
>                 for(m=0; m<DIM; m++)
>                 {
>                     vir[j][m] -= 0.5*f[j]*r_ij[g][m];
>                 }
>             }
> Can it be done in a similar way for the distance restraints?
> 
> Thanks, Alex