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<p class="MsoListParagraph" style="text-indent:-.25in;mso-list:l0 level1 lfo1"><![if !supportLists]><span style="font-family:Wingdings"><span style="mso-list:Ignore">Ø<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]>I actually want to do calculations between lambda steps inside of GROMACS code, before the end of the simulation.<o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri">“calculations” is a bit vague, as is “between lambda steps”. Can you be more specific?
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri">Best,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri;color:black">~~~~~~~~~~~~~~~~<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri;color:black">Michael Shirts<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri;color:black">Associate Professor<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri;color:black"><a href="mailto:michael.shirts@colorado.edu">michael.shirts@colorado.edu</a><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri;color:black"><a href="http://www.colorado.edu/lab/shirtsgroup/"><span style="text-decoration:none">http://www.colorado.edu/lab/shirtsgroup/</span></a><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri;color:black">Phone: (303) 735-7860<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri;color:black">Office: JSCBB C123<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri;color:black">Department of Chemical and Biological Engineering<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri;color:black">University of Colorado Boulder</span><span style="font-size:11.0pt;font-family:Calibri"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-family:Calibri;color:black">From: </span>
</b><span style="font-family:Calibri;color:black"><gromacs.org_gmx-developers-bounces@maillist.sys.kth.se> on behalf of "Mirabzadeh, Christopher (mira2978@vandals.uidaho.edu)" <mira2978@vandals.uidaho.edu><br>
<b>Reply-To: </b>"gmx-developers@gromacs.org" <gmx-developers@gromacs.org><br>
<b>Date: </b>Thursday, April 20, 2017 at 5:19 PM<br>
<b>To: </b>"gmx-developers@gromacs.org" <gmx-developers@gromacs.org><br>
<b>Subject: </b>Re: [gmx-developers] energy difference for lambda in free energy calculations<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Hello. Thanks! <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">I actually want to do calculations between lambda steps inside of GROMACS code, before the end of the simulation.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">-ChrisM<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt">Mirabzadeh, Christopher <br>
Graduate Research Assistant/Physics Instructor<br>
Department of Physics<br>
University of Idaho<br>
Moscow, Id<br>
(509)339-5647<br>
<br>
<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
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<p class="MsoNormal">On Apr 20, 2017, at 4:14 PM, Michael R Shirts <<a href="mailto:Michael.Shirts@Colorado.EDU">Michael.Shirts@Colorado.EDU</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:11.0pt;font-family:Calibri">Hi, Chris-</span><o:p></o:p></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:11.0pt;font-family:Calibri"> </span><o:p></o:p></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:11.0pt;font-family:Calibri">So, the dhdl.xvg output prints the potential energy difference between neighboring simulations (for BAR, MBAR, etc.), and the dh/dl values (for TI). So that file
should have all the information you need for any method – you can see the<span class="apple-converted-space"> </span><a href="https://github.com/MobleyLab/alchemical-analysis/"><span style="color:#954F72">https://github.com/MobleyLab/alchemical-analysis/</span></a><span class="apple-converted-space"> </span>scripts
for how this information is used.</span><o:p></o:p></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:11.0pt;font-family:Calibri"> </span><o:p></o:p></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:11.0pt;font-family:Calibri">The ROUTE to getting the values right is rather complicated for a number of reasons. So before answering in more detail-</span><o:p></o:p></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:11.0pt;font-family:Calibri"> </span><o:p></o:p></p>
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<p class="MsoNormal" style="text-indent:-.25in;background:white"><span style="font-size:11.0pt;font-family:Calibri">1.</span><span style="font-size:7.0pt"> <span class="apple-converted-space"> </span></span><span style="font-size:11.0pt;font-family:Calibri">If
you want to just USE this information, it’s all output by GROMACS already.</span><o:p></o:p></p>
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<p class="MsoNormal" style="text-indent:-.25in;background:white"><span style="font-size:11.0pt;font-family:Calibri">2.</span><span style="font-size:7.0pt"> <span class="apple-converted-space"> </span></span><span style="font-size:11.0pt;font-family:Calibri">If
you want to MODIFY what GROMACS is outputting, can you be more specific what you want to do?</span><o:p></o:p></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:11.0pt;font-family:Calibri"> </span><o:p></o:p></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:11.0pt;font-family:Calibri">~~~~~~~~~~~~~~~~</span><o:p></o:p></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:11.0pt;font-family:Calibri">Michael Shirts</span><o:p></o:p></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:11.0pt;font-family:Calibri">Associate Professor</span><o:p></o:p></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:11.0pt;font-family:Calibri"><a href="mailto:michael.shirts@colorado.edu">michael.shirts@colorado.edu</a></span><o:p></o:p></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:11.0pt;font-family:Calibri"><a href="http://www.colorado.edu/lab/shirtsgroup/"><span style="text-decoration:none">http://www.colorado.edu/lab/shirtsgroup/</span></a></span><o:p></o:p></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:11.0pt;font-family:Calibri">Phone: (303) 735-7860</span><o:p></o:p></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:11.0pt;font-family:Calibri">Office: JSCBB C123</span><o:p></o:p></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:11.0pt;font-family:Calibri">Department of Chemical and Biological Engineering</span><o:p></o:p></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:11.0pt;font-family:Calibri">University of Colorado Boulder</span><o:p></o:p></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:11.0pt;font-family:Calibri"> </span><o:p></o:p></p>
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<p class="MsoNormal" style="background:white"><b><span style="font-family:Calibri">From:<span class="apple-converted-space"> </span></span></b><span style="font-family:Calibri"><<a href="mailto:gromacs.org_gmx-developers-bounces@maillist.sys.kth.se"><span style="color:#954F72">gromacs.org_gmx-developers-bounces@maillist.sys.kth.se</span></a>>
on behalf of "Mirabzadeh, Christopher (<a href="mailto:mira2978@vandals.uidaho.edu"><span style="color:#954F72">mira2978@vandals.uidaho.edu</span></a>)" <<a href="mailto:mira2978@vandals.uidaho.edu"><span style="color:#954F72">mira2978@vandals.uidaho.edu</span></a>><br>
<b>Reply-To:<span class="apple-converted-space"> </span></b>"<a href="mailto:gmx-developers@gromacs.org"><span style="color:#954F72">gmx-developers@gromacs.org</span></a>" <<a href="mailto:gmx-developers@gromacs.org"><span style="color:#954F72">gmx-developers@gromacs.org</span></a>><br>
<b>Date:<span class="apple-converted-space"> </span></b>Thursday, April 20, 2017 at 5:01 PM<br>
<b>To:<span class="apple-converted-space"> </span></b>"<a href="mailto:gmx-developers@gromacs.org"><span style="color:#954F72">gmx-developers@gromacs.org</span></a>" <<a href="mailto:gmx-developers@gromacs.org"><span style="color:#954F72">gmx-developers@gromacs.org</span></a>><br>
<b>Subject:<span class="apple-converted-space"> </span></b>[gmx-developers] energy difference for lambda in free energy calculations</span><o:p></o:p></p>
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<p class="MsoNormal" style="background:white"> <o:p></o:p></p>
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<p class="MsoNormal" style="background:white">Hello all,<span class="apple-converted-space"> </span><o:p></o:p></p>
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<p class="MsoNormal" style="background:white"> <o:p></o:p></p>
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<p class="MsoNormal" style="background:white">What I’m trying to do is get the energy difference between neighboring expanded ensemble simulations, i.e U(lambda_trial, x) - U(lambda_current, x). As such, I am trying to better understand the de term used in
expanded ensemble calculations (de = weighted_lamee[lamtrial] - weighted_lamee[fep_state]). <o:p></o:p></p>
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<p class="MsoNormal" style="background:white"> <o:p></o:p></p>
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<p class="MsoNormal" style="background:white">It is defined in forcerec.h as:<o:p></o:p></p>
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<p class="MsoNormal" style="background:white"> <o:p></o:p></p>
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<p class="MsoNormal" style="background:white">typedef struct {<o:p></o:p></p>
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<p class="MsoNormal" style="background:white"> real term[F_NRE]; /* The energies for all different interaction types */<o:p></o:p></p>
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<p class="MsoNormal" style="background:white"> gmx_grppairener_t grpp;<o:p></o:p></p>
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<p class="MsoNormal" style="background:white"> double dvdl_lin[efptNR]; /* Contributions to dvdl with linear lam-dependence */<o:p></o:p></p>
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<p class="MsoNormal" style="background:white"> double dvdl_nonlin[efptNR]; /* Idem, but non-linear dependence */<o:p></o:p></p>
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<p class="MsoNormal" style="background:white"> int n_lambda;<o:p></o:p></p>
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<p class="MsoNormal" style="background:white"> int fep_state; /*current fep state -- just for printing */<o:p></o:p></p>
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<p class="MsoNormal" style="background:white"><span style="color:#FF2600"> double *enerpart_lambda; /* Partial energy for lambda and flambda[] */</span><o:p></o:p></p>
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<p class="MsoNormal" style="background:white"> real foreign_term[F_NRE]; /* alternate array for storing foreign lambda energies */<o:p></o:p></p>
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<p class="MsoNormal" style="background:white"> gmx_grppairener_t foreign_grpp; /* alternate array for storing foreign lambda energies */<o:p></o:p></p>
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<p class="MsoNormal" style="background:white">} gmx_enerdata_t;<o:p></o:p></p>
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<p class="MsoNormal" style="background:white">/* The idea is that dvdl terms with linear lambda dependence will be added<o:p></o:p></p>
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<p class="MsoNormal" style="background:white"> * automatically to enerpart_lambda. Terms with non-linear lambda dependence<o:p></o:p></p>
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<p class="MsoNormal" style="background:white"> * should explicitly determine the energies at foreign lambda points<o:p></o:p></p>
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<p class="MsoNormal" style="background:white"> * when n_lambda > 0.<o:p></o:p></p>
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<p class="MsoNormal" style="background:white"> */<o:p></o:p></p>
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<p class="MsoNormal" style="background:white"> <o:p></o:p></p>
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<p class="MsoNormal" style="background:white">I see that this term is used in the xvg output inside of mdebin.c and <o:p></o:p></p>
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<p class="MsoNormal" style="background:white"> <o:p></o:p></p>
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<p class="MsoNormal" style="background:white"> /* BAR + thermodynamic integration values */<o:p></o:p></p>
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<p class="MsoNormal" style="background:white"> if ((md->fp_dhdl || md->dhc) && bDoDHDL)<o:p></o:p></p>
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<p class="MsoNormal" style="background:white"> {<o:p></o:p></p>
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<p class="MsoNormal" style="background:white"> for (i = 0; i < enerd->n_lambda-1; i++)<o:p></o:p></p>
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<p class="MsoNormal" style="background:white"> {<o:p></o:p></p>
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<p class="MsoNormal" style="background:white"> /* zero for simulated tempering */<o:p></o:p></p>
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<p class="MsoNormal" style="background:white"> md->dE[i] = enerd->enerpart_lambda[i+1]-enerd->enerpart_lambda[0];<o:p></o:p></p>
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<p class="MsoNormal" style="background:white">……<o:p></o:p></p>
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<p class="MsoNormal" style="background:white"> <o:p></o:p></p>
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<p class="MsoNormal" style="background:white">Also, in the replica exchange code (repl_ex.c) we find this term again;<o:p></o:p></p>
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<p class="MsoNormal" style="background:white"> <o:p></o:p></p>
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<p class="MsoNormal" style="background:white"> if (re->type == ereLAMBDA || re->type == ereTL)<o:p></o:p></p>
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<p class="MsoNormal" style="background:white"> {<o:p></o:p></p>
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<p class="MsoNormal" style="background:white"> bDLambda = TRUE;<o:p></o:p></p>
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<p class="MsoNormal" style="background:white"> /* lambda differences. */<o:p></o:p></p>
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<p class="MsoNormal" style="background:white"> /* de[i][j] is the energy of the jth simulation in the ith Hamiltonian<o:p></o:p></p>
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<p class="MsoNormal" style="background:white"> minus the energy of the jth simulation in the jth Hamiltonian */<o:p></o:p></p>
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<p class="MsoNormal" style="background:white"> for (i = 0; i < re->nrepl; i++)<o:p></o:p></p>
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<p class="MsoNormal" style="background:white"> {<o:p></o:p></p>
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<p class="MsoNormal" style="background:white"> for (j = 0; j < re->nrepl; j++)<o:p></o:p></p>
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<p class="MsoNormal" style="background:white"> {<o:p></o:p></p>
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<p class="MsoNormal" style="background:white"> re->de[i][j] = 0;<o:p></o:p></p>
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<p class="MsoNormal" style="background:white"> }<o:p></o:p></p>
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<p class="MsoNormal" style="background:white"> }<o:p></o:p></p>
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<p class="MsoNormal" style="background:white"> for (i = 0; i < re->nrepl; i++)<o:p></o:p></p>
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<p class="MsoNormal" style="background:white"> {<o:p></o:p></p>
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<p class="MsoNormal" style="background:white"> re->de[i][re->repl] = (enerd->enerpart_lambda[(int)re->q[ereLAMBDA][i]+1]-enerd->enerpart_lambda[0]);<o:p></o:p></p>
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<p class="MsoNormal" style="background:white"> ……<o:p></o:p></p>
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<p class="MsoNormal" style="background:white"> <o:p></o:p></p>
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<p class="MsoNormal" style="background:white"> <o:p></o:p></p>
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<p class="MsoNormal" style="background:white"> <o:p></o:p></p>
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<p class="MsoNormal" style="background:white">I’m trying to understand how this term is used in Thermodynamic integration (Pymbar for instance). Also, I’ve noticed that the enerd->enerpart_lambda[0] term is only updated every nstenergy step. Could anyone explain
what the 0 term is and how this enerpart_lambda[i]-enerpart_lambda[0] term would be used in TI? <o:p></o:p></p>
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<p class="MsoNormal" style="background:white"> <o:p></o:p></p>
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<p class="MsoNormal" style="background:white">The bottom line is that I need the correct value for the energy difference between neighboring lambda simulations. Does the de term do that for me? <o:p></o:p></p>
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<p class="MsoNormal" style="background:white"> <o:p></o:p></p>
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<p class="MsoNormal" style="background:white">If de is the correct term, is delta lambda part of the calculation? The reason I ask this question is from not understanding the output of debug information in force.c, specifically;<o:p></o:p></p>
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<p class="MsoNormal" style="background:white"> <o:p></o:p></p>
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<p class="MsoNormal" style="background:white"> if (debug)<o:p></o:p></p>
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<p class="MsoNormal" style="background:white"> {<o:p></o:p></p>
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<p class="MsoNormal" style="background:white"> fprintf(debug, "enerdiff lam %g: (%15s), non-linear %f linear %f*%f\n",<o:p></o:p></p>
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<p class="MsoNormal" style="background:white"> fepvals->all_lambda[j][i], efpt_names[j],<o:p></o:p></p>
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<p class="MsoNormal" style="background:white"> (enerd->enerpart_lambda[i+1] - enerd->enerpart_lambda[0]),<o:p></o:p></p>
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<p class="MsoNormal" style="background:white"> dlam, enerd->dvdl_lin[j]);<o:p></o:p></p>
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<p class="MsoNormal" style="background:white"> }<o:p></o:p></p>
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<p class="MsoNormal" style="background:white"> <o:p></o:p></p>
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<p class="MsoNormal" style="background:white">Does this mean that the energy difference is (enerd->enerpart_lambda[i+1] - enerd->enerpart_lambda[0]) + dlam*dvdl_lin[i]? I’m very confused.<o:p></o:p></p>
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<p class="MsoNormal" style="background:white"> <o:p></o:p></p>
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<p class="MsoNormal" style="background:white"> <o:p></o:p></p>
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<p class="MsoNormal" style="background:white">Thanks,<o:p></o:p></p>
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<p class="MsoNormal" style="background:white"> <o:p></o:p></p>
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<p class="MsoNormal" style="background:white">-ChrisM<o:p></o:p></p>
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<p class="MsoNormal" style="background:white"> <o:p></o:p></p>
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<div>
<p class="MsoNormal" style="margin-bottom:12.0pt;background:white">Mirabzadeh, Christopher <br>
Graduate Research Assistant/Physics Instructor<br>
Department of Physics<br>
University of Idaho<br>
Moscow, Id<br>
(509)339-5647<br>
<br>
<br>
<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="background:white"> <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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