On 12/26/17 7:53 AM, Mandar Kulkarni wrote:
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
|Zmax-Zmin|
will be constant, is it correct to assume fixed minimum(Zmin) and
maximum(Zmax) limits?
Such calculations are usually performed with a static z-dimension, e.g
incompressible along that axis. In that case, Zmin and Zmax are (and
should be) fixed.
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?
You shouldn't have to use any complex trjconv command. Just make
molecules whole and that should be correct. No additional centering is
required; your molecules stay in the central volume anyway, and you
don't want to shift coordinates when relying on fixed points in space
for computing your osmotic pressure forces.
-Justin
3. The GROMACS source code section below calculates flat-bottom restraint
forces
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
--
==
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
==
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