[gmx-developers] Flat-bottom position restraints: printing of instantaneous forces

[Justin Lemkul]

On 11/13/17 1:26 AM, Mandar Kulkarni wrote:
> Dear Gromacs Developers,
> I am running osmotic pressure simulation using GROMACS 5.0.7 version. 
> I am applying flat-bottom potential similar to the work of Lay et al. 
> (J. Chem Theory Comput., 2016,12, 1401).
>
> I have provided reference pdb which has Z-coordinates of solute atoms 
> to be restrained are set to the value of  half of the box length in 
> Z-direction and layer like potential is applied using posre.itp with a 
> format shown below:
> [ position_restraints ]
> ;  i funct      g    r    k
>    1    2      5    2.8    1000
>
> I would like to print instantaneous force acting on the wall due to 
> solute atoms while running a simulation. I guess that forces are 
> calculated in "position-restraints.cpp" file and Line 293 gives the 
> total force acting on the wall for layer-like flat bottom potential.
>
> for (m = 0; (m < DIM); m++)
>         {
>             f[ai][m]   += fm[m];
>             /* Here we correct for the pbc_dx which included rdist */
>             vir_diag[m] -= 0.5*(dx[m] + rdist[m])*fm[m];
>         }
>
> Please, any guidance to implement printing of instantaneous forces 
> will be really helpful.
> Thanks in advance.
>
> (PS: I am sorry if this is answered previously, but I am unable to 
> find the similar discussions in archived threads.)
>

I wouldn't bother trying to hack the GROMACS source, just re-compute the 
force due to the restraint after the simulation, based on the 
z-coordinate over time. Extract the z-coordinates with gmx traj and 
post-process the frames with whatever code you like. It's a simple 
calculation.

-Justin

>
> Best Regards,
> Mandar Kulkarni
>
>
>
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==================================================

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-developers/attachments/20171116/fb29531e/attachment.html>