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<div class="moz-cite-prefix">On 11/13/17 1:26 AM, Mandar Kulkarni
wrote:<br>
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cite="mid:CAKC_24hKJ9qYYzrQoipSx2Ce0Q192KoGFRrnFFT8b3Q+ZUOkvw@mail.gmail.com">
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<div>Dear Gromacs Developers,<br>
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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).<br>
<br>
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:<br>
[ position_restraints ]<br>
; i funct g r k<br>
1 2 5 2.8 1000<br>
<br>
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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.<br>
<br>
for (m = 0; (m < DIM); m++)<br>
{<br>
f[ai][m] += fm[m];<br>
/* Here we correct for the pbc_dx which included
rdist */<br>
vir_diag[m] -= 0.5*(dx[m] + rdist[m])*fm[m];<br>
}<br>
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Please, any guidance to implement printing of instantaneous
forces will be really helpful.<br>
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<div>Thanks in advance.<br>
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<div><br>
(PS: I am sorry if this is answered previously, but I am
unable to find the similar discussions in archived threads.)<br>
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<br>
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.<br>
<br>
-Justin<br>
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<div dir="ltr"><font
face="arial,
helvetica,
sans-serif"
size="2"><font
style="background-color:rgb(255,255,255)"><font
color="#000000"><span></span><span></span></font><span
style="font-family:monospace,monospace"><span
style="color:rgb(0,0,255)"><span
style="background-color:rgb(255,255,255)">Best
Regards</span>,<br>
Mandar
Kulkarni</span></span></font><span
style="font-family:monospace,monospace"><span style="color:rgb(0,0,255)">
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<pre class="moz-signature" cols="72">--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
<a class="moz-txt-link-abbreviated" href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a> | (540) 231-3129
<a class="moz-txt-link-freetext" href="http://www.biochem.vt.edu/people/faculty/JustinLemkul.html">http://www.biochem.vt.edu/people/faculty/JustinLemkul.html</a>
==================================================
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