<div dir="ltr"><div>Thanks a lot for your response.<br>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.<br>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. <br></div><div><br></div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><font size="2" face="arial, helvetica, sans-serif"><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)"> <br></span></span></font><div><font size="2"><span style="font-family:monospace,monospace"><span style="color:rgb(0,0,255)"><span style="background-color:rgb(255,255,255)"></span>Postdoctoral Research Fellow,<br></span></span></font></div><div><font size="2"><span style="font-family:monospace,monospace"><span style="color:rgb(0,0,255)">Department of Chemistry,<br></span></span></font></div><div><font size="2"><span style="font-family:monospace,monospace"><span style="color:rgb(0,0,255)">Pusan National University,</span></span></font></div><div><span style="color:rgb(0,0,255)"><font size="2" face="arial, helvetica, sans-serif"><span style="font-family:monospace,monospace">Busan, South Korea</span><br></font></span><br></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
<br><div class="gmail_quote">On Fri, Nov 17, 2017 at 8:00 PM, <span dir="ltr"><<a href="mailto:gromacs.org_gmx-developers-request@maillist.sys.kth.se" target="_blank">gromacs.org_gmx-developers-request@maillist.sys.kth.se</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Send gromacs.org_gmx-developers mailing list submissions to<br>
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Today's Topics:<br>
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1. Re: Flat-bottom position restraints: printing of<br>
instantaneous forces (Justin Lemkul)<br>
<br>
<br>
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<br>
Message: 1<br>
Date: Thu, 16 Nov 2017 08:05:18 -0500<br>
From: Justin Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
To: <a href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a><br>
Subject: Re: [gmx-developers] Flat-bottom position restraints:<br>
printing of instantaneous forces<br>
Message-ID: <<a href="mailto:b52cfa65-c9c1-21ed-5642-084fc8853512@vt.edu">b52cfa65-c9c1-21ed-5642-<wbr>084fc8853512@vt.edu</a>><br>
Content-Type: text/plain; charset="utf-8"; Format="flowed"<br>
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<br>
On 11/13/17 1:26 AM, Mandar Kulkarni wrote:<br>
> Dear Gromacs Developers,<br>
> I am running osmotic pressure simulation using GROMACS 5.0.7 version.<br>
> I am applying flat-bottom potential similar to the work of Lay et al.<br>
> (J. Chem Theory Comput., 2016,12, 1401).<br>
><br>
> I have provided reference pdb which has Z-coordinates of solute atoms<br>
> to be restrained are set to the value of? half of the box length in<br>
> Z-direction and layer like potential is applied using posre.itp with a<br>
> format shown below:<br>
> [ position_restraints ]<br>
> ;? i funct????? g??? r??? k<br>
> ?? 1??? 2????? 5??? 2.8??? 1000<br>
><br>
> I would like to print instantaneous force acting on the wall due to<br>
> solute atoms while running a simulation. I guess that forces are<br>
> calculated in "position-restraints.cpp" file and Line 293 gives the<br>
> 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>
><br>
> Please, any guidance to implement printing of instantaneous forces<br>
> will be really helpful.<br>
> Thanks in advance.<br>
><br>
> (PS: I am sorry if this is answered previously, but I am unable to<br>
> find the similar discussions in archived threads.)<br>
><br>
<br>
I wouldn't bother trying to hack the GROMACS source, just re-compute the<br>
force due to the restraint after the simulation, based on the<br>
z-coordinate over time. Extract the z-coordinates with gmx traj and<br>
post-process the frames with whatever code you like. It's a simple<br>
calculation.<br>
<br>
-Justin<br>
<br>
><br>
> Best Regards,<br>
> Mandar Kulkarni<br>
><br>
><br>
><br>
><br>
<br>
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==============================<wbr>====================<br>
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Justin A. Lemkul, Ph.D.<br>
Assistant Professor<br>
Virginia Tech Department of Biochemistry<br>
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<a href="http://www.biochem.vt.edu/people/faculty/JustinLemkul.html" rel="noreferrer" target="_blank">http://www.biochem.vt.edu/<wbr>people/faculty/JustinLemkul.<wbr>html</a><br>
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