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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Dear Dr. <span style="font-size: small;">Feenstra K.A</span>
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<div><font size="2">Thank you very much for your response.</font></div>
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<div><font size="2">What I'm trying to achieve is explained at:</font></div>
<div><a href="http://arxiv.org/abs/1307.1620" target="_blank">http://arxiv.org/abs/1307.1620</a></div>
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<div>In short, if it is combined with multiplication by lambda=[0,1] it is supposed to come instead of the chance in the VDW and electric potential that is associated with "annihilation". If Ec will have value of around 7kCal/mole I think that it should have
negligible effect on the free energy at lambda=1.</div>
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<div>Do you know if it is explained in the manual also how to multiply VDW and electric forces (<span style="font-size: 10pt;">that are associated with certian atoms)</span><span style="font-size: 10pt;"> by a const ?</span></div>
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<div>Thanks again,</div>
<div>Best regards,</div>
<div>Asaf</div>
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<div id="divRpF585952" style="direction: ltr;"><font face="Tahoma" size="2" color="#000000"><b>From:</b> gmx-developers-bounces@gromacs.org [gmx-developers-bounces@gromacs.org] on behalf of Feenstra, K.A. [k.a.feenstra@vu.nl]<br>
<b>Sent:</b> Friday, August 30, 2013 10:02 AM<br>
<b>To:</b> Discussion list for GROMACS development<br>
<b>Cc:</b> Discussion list for GROMACS development<br>
<b>Subject:</b> Re: [gmx-developers] editing the code of the VDW and electric potentials and forces<br>
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<div>Op 30 aug. 2013 om 08:49 heeft "Asaf Farhi" <<a href="mailto:asaf.farhi@weizmann.ac.il" target="_blank">asaf.farhi@weizmann.ac.il</a>> het volgende geschreven:<br>
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<div style="direction:ltr; font-family:Tahoma; color:#000000; font-size:10pt">Dear GROMACS Developers
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<div><span style="font-family:monospace; font-size:16px">My name is Asaf.</span><br style="font-family:monospace; font-size:16px">
<span style="font-family:monospace; font-size:16px">I'm trying to implement a novel free energy calculation method and interested to do a very minor code change.</span><br style="font-family:monospace; font-size:16px">
<span style="font-family:monospace; font-size:16px">I will really appreciate help on this issue.</span><br style="font-family:monospace; font-size:16px">
<span style="font-family:monospace; font-size:16px">What I'm trying to implement in GROMACS is very simple. It's actually only one if statement that is relevant to the VDW and Electric energies and forces.</span><br style="font-family:monospace; font-size:16px">
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<span style="font-family:monospace; font-size:16px">What is needed is to add for every calculation of energy and force:</span><br style="font-family:monospace; font-size:16px">
<span style="font-family:monospace; font-size:16px">If (E_VDW>Ec)</span><br style="font-family:monospace; font-size:16px">
<span style="font-family:monospace; font-size:16px">{</span><br style="font-family:monospace; font-size:16px">
<span style="font-family:monospace; font-size:16px">E_VDW=Ec;</span><br style="font-family:monospace; font-size:16px">
<span style="font-family:monospace; font-size:16px">f_VDW=0;</span><br style="font-family:monospace; font-size:16px">
<span style="font-family:monospace; font-size:16px">}</span><br style="font-family:monospace; font-size:16px">
<span style="font-family:monospace; font-size:16px">If (E_EL>Ec)</span><br style="font-family:monospace; font-size:16px">
<span style="font-family:monospace; font-size:16px">{</span><br style="font-family:monospace; font-size:16px">
<span style="font-family:monospace; font-size:16px">E_el=Ec;</span><br style="font-family:monospace; font-size:16px">
<span style="font-family:monospace; font-size:16px">f_el=0;</span><br style="font-family:monospace; font-size:16px">
<span style="font-family:monospace; font-size:16px">}</span><br style="font-family:monospace; font-size:16px">
<br style="font-family:monospace; font-size:16px">
<span style="font-family:monospace; font-size:16px">where E_VDW is the energy associated with the pair VDW interaction, f_VDW is the force associated with the pair VDW potential and Ec is a constant.</span><br style="font-family:monospace; font-size:16px">
<span style="font-family:monospace; font-size:16px">In addition I need to multiply specific VDW and electrical forces by a const (that are associated with certain atoms).</span></div>
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<div>Could anyone advise me how to do this code change?<br style="font-family:monospace; font-size:16px">
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<div>If I understand what you want to do, i.e. a fixed upper limit to the energies, than you could do that easily, without touching the code, bu using interaction tables. You will find how in the manual.</div>
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<div>What you haven't explained is what you want to achieve. </div>
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<div>The setup you describe will give an unphysical discontinuity in the forces, which will give rise to some strange artifacts in your simulations for sure. I expect these may be similar, in type and severity, to those associated with the simple interaction
cut-off schemes. Using that as a basis for '<span class="Apple-style-span" style="font-family: monospace;">a novel free energy calculation method'</span><span class="Apple-style-span" style=""> seems rather unlikely to produce valid results.</span></div>
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<span style="font-family:monospace; font-size:16px">Thanks in advance,</span><br style="font-family:monospace; font-size:16px">
<span style="font-family:monospace; font-size:16px">Best regards,</span><br style="font-family:monospace; font-size:16px">
<span style="font-family:monospace; font-size:16px">Asaf</span><br style="font-family:monospace; font-size:16px">
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