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

[Mark Abraham]

Hi,

See e.g. the use of fshift in ta_disres in disre.c. These "shift forces" go
into the virial calculation, see Appendix B of the manual.

Mark

On Fri, May 8, 2015 at 10:49 AM Berk Hess <hess at kth.se> wrote:

> Hi,
>
> No normal interactions are explicitly listed in calcvir.
> Anything forces that are added to the normal force buffer (and
> fr->fshift) before calc_virial is called are accounted for "automatically".
>
> Berk
>
> On 2015-05-08 10:37, Alexander Kuhn wrote:
> > 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
>
> --
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