[gmx-users] Osmotic Pressure Calculations and fixed reference values of walls

Mandar Kulkarni mandarkulkarni at pusan.ac.kr
Tue Dec 26 14:53:54 CET 2017

Dear All,
I am performing osmotic pressure simulations using 30 nucleoside molecules
using 1D flat bottom restraints along Z-axis(Zmin and Zmax). I am using
GROMACS 5.0.7 version and reference coordinates are provided using -r
option in grompp.
The osmotic pressure runs are performed under NPT conditions with
semi-isotropic pressure coupling. I am calculating osmotic pressure using
C-program which simply calculates forces on heavy atoms of nucleosides
attempting to cross the Zmin and Zmax limits.

I have searched archived posts, however, I am confused about possible
implementation and post-processing in the present case. Any help will be
really helpful to solve the following issues.

1. The upper and lower limits of the flat bottom restraints are defined
while starting the simulations using static reference frame. Although
will be constant, is it correct to assume fixed minimum(Zmin) and
maximum(Zmax) limits?

2. During post-processing when one centers the trajectory and correct PBC
for nucleoside molecules (trjconv -pbc mol -ur compact -center options), is
it appropriate to assume the same Zmin and Zmax values at t=0 throughout
the analysis?

3. The GROMACS source code section below calculates flat-bottom restraint

     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];


How can we print force f[ai][m] at each time step to separate file? I
assume it might be not straightforward to print these forces, but a short
general guideline might help me to achieve the objective.

Sorry for so many questions and Thanks in advance.
Also, Wish you all happy new year in advance.

Best Regards,
Mandar Kulkarni,
Pusan National University, South Korea

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