[gmx-developers] gromacs.org_gmx-developers Digest, Vol 163, Issue 17

[Mandar Kulkarni]

Thanks a lot for your response.
Currently, I am using gmx traj and a C-program to calculate osmotic
pressure. My test calculations for NaCl ions matches the previous study of
Luo and Roux.
The study by Lay et al. mentions minor modification ( J. Chem Theory
Comput., 2016,12, 1401) in GROMACS source code. I thought it would be
efficient to print these values on the fly. Thanks once again.


Best Regards,
Mandar Kulkarni
Postdoctoral Research Fellow,
Department of Chemistry,
Pusan National University,
Busan, South Korea


On Fri, Nov 17, 2017 at 8:00 PM, <
gromacs.org_gmx-developers-request at maillist.sys.kth.se> wrote:

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>    1. Re: Flat-bottom position restraints: printing of
>       instantaneous forces (Justin Lemkul)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 16 Nov 2017 08:05:18 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-developers at gromacs.org
> Subject: Re: [gmx-developers] Flat-bottom position restraints:
>         printing of instantaneous forces
> Message-ID: <b52cfa65-c9c1-21ed-5642-084fc8853512 at vt.edu>
> Content-Type: text/plain; charset="utf-8"; Format="flowed"
>
>
>
> 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
>
> ==================================================
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