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Fair enough. Specifically I want the energy difference between lambda steps in order to incorporate the adaptive integration method (AIM) inside of GROMACS.
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<div class=""><a href="http://redmine.gromacs.org/issues/1849" class="">http://redmine.gromacs.org/issues/1849</a></div>
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<div class="">I need the de term as part of the acceptance criteria for the Monte Carlo moves between lambda steps. I’ve been working on this for a while now and thought I had things working correctly last year until I dissected the alchemical-analysis code
and found that I wasn’t properly accounting for the individual delta lambda terms. AIM uses the same integral as TI in it’s acceptance criteria. AIM also uses the difference between neighboring lambda simulations, thus the acceptance criteria is:</div>
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<div class="">exp(-de + df) </div>
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<div class="">where I’m calculating df as:</div>
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<div class=""> for (j=0; j < efptNR; j++)</div>
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<div class=""> if (fep->separate_dvdl[j])</div>
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<div class=""> // integrate from fep_state to lamtrial</div>
<div class=""> df += 0.5</div>
<div class=""> * (fep->all_lambda[j][lamtrial] - fep->all_lambda[j][fep_state])</div>
<div class=""> * (dfhist->sum_dvdl[j][lamtrial] + dfhist->sum_dvdl[j][fep_state])</div>
<div class=""> * (1.0/expand->mc_temp*BOLTZ);</div>
<div class=""> }</div>
<div class=""> }</div>
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<div class="">Based on comparisons with the output of TI, I believe I’m calculating df correctly but my histogram isn’t flat and my estimate for the free energy is low. I’m trying to make sure I’m using the correct value for de within my acceptance criteria.</div>
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<div class="">Is that better?</div>
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<div class="">Cheers,</div>
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<div class="">-ChrisM</div>
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<div class="">Mirabzadeh, Christopher <br class="">
Graduate Research Assistant/Physics Instructor<br class="">
Department of Physics<br class="">
University of Idaho<br class="">
Moscow, Id<br class="">
(509)339-5647<br class="">
<br class="">
<br class="">
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<blockquote type="cite" class="">
<div class="">On Apr 20, 2017, at 4:23 PM, Michael R Shirts <<a href="mailto:Michael.Shirts@Colorado.EDU" class="">Michael.Shirts@Colorado.EDU</a>> wrote:</div>
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<div class="WordSection1" style="page: WordSection1; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);">
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<span style="font-family: Wingdings;" class=""><span class="">Ø<span style="font-style: normal; font-variant-caps: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-family: 'Times New Roman';" class=""> <span class="Apple-converted-space"> </span></span></span></span>I
actually want to do calculations between lambda steps inside of GROMACS code, before the end of the simulation.<o:p class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri;" class=""><o:p class=""> </o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri;" class="">“calculations” is a bit vague, as is “between lambda steps”. Can you be more specific?<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri;" class=""><o:p class=""> </o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri;" class="">Best,<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri;" class="">~~~~~~~~~~~~~~~~<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri;" class="">Michael Shirts<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri;" class="">Associate Professor<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri;" class=""><a href="mailto:michael.shirts@colorado.edu" style="color: purple; text-decoration: underline;" class="">michael.shirts@colorado.edu</a><o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri;" class="">Phone: (303) 735-7860<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri;" class="">Office: JSCBB C123<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri;" class="">Department of Chemical and Biological Engineering<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri;" class="">University of Colorado Boulder</span><span style="font-size: 11pt; font-family: Calibri;" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri;" class=""><o:p class=""> </o:p></span></div>
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<b class=""><span style="font-family: Calibri;" class="">From:<span class="Apple-converted-space"> </span></span></b><span style="font-family: Calibri;" class=""><<a href="mailto:gromacs.org_gmx-developers-bounces@maillist.sys.kth.se" class="">gromacs.org_gmx-developers-bounces@maillist.sys.kth.se</a>>
on behalf of "Mirabzadeh, Christopher (<a href="mailto:mira2978@vandals.uidaho.edu" class="">mira2978@vandals.uidaho.edu</a>)" <<a href="mailto:mira2978@vandals.uidaho.edu" class="">mira2978@vandals.uidaho.edu</a>><br class="">
<b class="">Reply-To:<span class="Apple-converted-space"> </span></b>"<a href="mailto:gmx-developers@gromacs.org" class="">gmx-developers@gromacs.org</a>" <<a href="mailto:gmx-developers@gromacs.org" class="">gmx-developers@gromacs.org</a>><br class="">
<b class="">Date:<span class="Apple-converted-space"> </span></b>Thursday, April 20, 2017 at 5:19 PM<br class="">
<b class="">To:<span class="Apple-converted-space"> </span></b>"<a href="mailto:gmx-developers@gromacs.org" class="">gmx-developers@gromacs.org</a>" <<a href="mailto:gmx-developers@gromacs.org" class="">gmx-developers@gromacs.org</a>><br class="">
<b class="">Subject:<span class="Apple-converted-space"> </span></b>Re: [gmx-developers] energy difference for lambda in free energy calculations<o:p class=""></o:p></span></div>
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<o:p class=""> </o:p></div>
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Hello. Thanks!<span class="Apple-converted-space"> </span><o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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I actually want to do calculations between lambda steps inside of GROMACS code, before the end of the simulation.<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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-ChrisM<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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Mirabzadeh, Christopher <br class="">
Graduate Research Assistant/Physics Instructor<br class="">
Department of Physics<br class="">
University of Idaho<br class="">
Moscow, Id<br class="">
(509)339-5647<br class="">
<br class="">
<o:p class=""></o:p></p>
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<o:p class=""> </o:p></div>
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On Apr 20, 2017, at 4:14 PM, Michael R Shirts <<a href="mailto:Michael.Shirts@Colorado.EDU" style="color: purple; text-decoration: underline;" class="">Michael.Shirts@Colorado.EDU</a>> wrote:<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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<span style="font-size: 11pt; font-family: Calibri;" class="">Hi, Chris-</span><o:p class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri;" class=""> </span><o:p class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri;" class="">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/" style="color: purple; text-decoration: underline;" class=""><span style="color: rgb(149, 79, 114);" class="">https://github.com/MobleyLab/alchemical-analysis/</span></a><span class="apple-converted-space"> </span>scripts
for how this information is used.</span><o:p class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri;" class=""> </span><o:p class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri;" class="">The ROUTE to getting the values right is rather complicated for a number of reasons. So before answering in more detail-</span><o:p class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri;" class=""> </span><o:p class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri;" class="">1.</span><span style="font-size: 7pt;" class=""> <span class="apple-converted-space"> </span></span><span style="font-size: 11pt; font-family: Calibri;" class="">If you want to just USE this
information, it’s all output by GROMACS already.</span><o:p class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri;" class="">2.</span><span style="font-size: 7pt;" class=""> <span class="apple-converted-space"> </span></span><span style="font-size: 11pt; font-family: Calibri;" class="">If you want to MODIFY what GROMACS
is outputting, can you be more specific what you want to do?</span><o:p class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri;" class=""> </span><o:p class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri;" class="">~~~~~~~~~~~~~~~~</span><o:p class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri;" class="">Michael Shirts</span><o:p class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri;" class="">Associate Professor</span><o:p class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri;" class=""><a href="mailto:michael.shirts@colorado.edu" style="color: purple; text-decoration: underline;" class="">michael.shirts@colorado.edu</a></span><o:p class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri;" class=""><a href="http://www.colorado.edu/lab/shirtsgroup/" style="color: purple; text-decoration: underline;" class=""><span style="text-decoration: none;" class="">http://www.colorado.edu/lab/shirtsgroup/</span></a></span><o:p class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri;" class="">Phone: (303) 735-7860</span><o:p class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri;" class="">Office: JSCBB C123</span><o:p class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri;" class="">Department of Chemical and Biological Engineering</span><o:p class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri;" class="">University of Colorado Boulder</span><o:p class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri;" class=""> </span><o:p class=""></o:p></div>
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<b class=""><span style="font-family: Calibri;" class="">From:<span class="apple-converted-space"> </span></span></b><span style="font-family: Calibri;" class=""><<a href="mailto:gromacs.org_gmx-developers-bounces@maillist.sys.kth.se" style="color: purple; text-decoration: underline;" class=""><span style="color: rgb(149, 79, 114);" class="">gromacs.org_gmx-developers-bounces@maillist.sys.kth.se</span></a>>
on behalf of "Mirabzadeh, Christopher (<a href="mailto:mira2978@vandals.uidaho.edu" style="color: purple; text-decoration: underline;" class=""><span style="color: rgb(149, 79, 114);" class="">mira2978@vandals.uidaho.edu</span></a>)" <<a href="mailto:mira2978@vandals.uidaho.edu" style="color: purple; text-decoration: underline;" class=""><span style="color: rgb(149, 79, 114);" class="">mira2978@vandals.uidaho.edu</span></a>><br class="">
<b class="">Reply-To:<span class="apple-converted-space"> </span></b>"<a href="mailto:gmx-developers@gromacs.org" style="color: purple; text-decoration: underline;" class=""><span style="color: rgb(149, 79, 114);" class="">gmx-developers@gromacs.org</span></a>"
<<a href="mailto:gmx-developers@gromacs.org" style="color: purple; text-decoration: underline;" class=""><span style="color: rgb(149, 79, 114);" class="">gmx-developers@gromacs.org</span></a>><br class="">
<b class="">Date:<span class="apple-converted-space"> </span></b>Thursday, April 20, 2017 at 5:01 PM<br class="">
<b class="">To:<span class="apple-converted-space"> </span></b>"<a href="mailto:gmx-developers@gromacs.org" style="color: purple; text-decoration: underline;" class=""><span style="color: rgb(149, 79, 114);" class="">gmx-developers@gromacs.org</span></a>" <<a href="mailto:gmx-developers@gromacs.org" style="color: purple; text-decoration: underline;" class=""><span style="color: rgb(149, 79, 114);" class="">gmx-developers@gromacs.org</span></a>><br class="">
<b class="">Subject:<span class="apple-converted-space"> </span></b>[gmx-developers] energy difference for lambda in free energy calculations</span><o:p class=""></o:p></div>
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Hello all,<span class="apple-converted-space"> </span><o:p class=""></o:p></div>
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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 class=""></o:p></div>
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It is defined in forcerec.h as:<o:p class=""></o:p></div>
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typedef struct {<o:p class=""></o:p></div>
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real term[F_NRE]; /* The energies for all different interaction types */<o:p class=""></o:p></div>
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gmx_grppairener_t grpp;<o:p class=""></o:p></div>
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double dvdl_lin[efptNR]; /* Contributions to dvdl with linear lam-dependence */<o:p class=""></o:p></div>
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double dvdl_nonlin[efptNR]; /* Idem, but non-linear dependence */<o:p class=""></o:p></div>
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int n_lambda;<o:p class=""></o:p></div>
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int fep_state; /*current fep state -- just for printing */<o:p class=""></o:p></div>
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<span style="color: rgb(255, 38, 0);" class=""> double *enerpart_lambda; /* Partial energy for lambda and flambda[] */</span><o:p class=""></o:p></div>
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real foreign_term[F_NRE]; /* alternate array for storing foreign lambda energies */<o:p class=""></o:p></div>
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gmx_grppairener_t foreign_grpp; /* alternate array for storing foreign lambda energies */<o:p class=""></o:p></div>
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} gmx_enerdata_t;<o:p class=""></o:p></div>
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/* The idea is that dvdl terms with linear lambda dependence will be added<o:p class=""></o:p></div>
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* automatically to enerpart_lambda. Terms with non-linear lambda dependence<o:p class=""></o:p></div>
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* should explicitly determine the energies at foreign lambda points<o:p class=""></o:p></div>
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* when n_lambda > 0.<o:p class=""></o:p></div>
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*/<o:p class=""></o:p></div>
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I see that this term is used in the xvg output inside of mdebin.c and <o:p class=""></o:p></div>
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/* BAR + thermodynamic integration values */<o:p class=""></o:p></div>
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if ((md->fp_dhdl || md->dhc) && bDoDHDL)<o:p class=""></o:p></div>
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{<o:p class=""></o:p></div>
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for (i = 0; i < enerd->n_lambda-1; i++)<o:p class=""></o:p></div>
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{<o:p class=""></o:p></div>
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/* zero for simulated tempering */<o:p class=""></o:p></div>
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md->dE[i] = enerd->enerpart_lambda[i+1]-enerd->enerpart_lambda[0];<o:p class=""></o:p></div>
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……<o:p class=""></o:p></div>
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Also, in the replica exchange code (repl_ex.c) we find this term again;<o:p class=""></o:p></div>
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if (re->type == ereLAMBDA || re->type == ereTL)<o:p class=""></o:p></div>
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{<o:p class=""></o:p></div>
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bDLambda = TRUE;<o:p class=""></o:p></div>
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/* lambda differences. */<o:p class=""></o:p></div>
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/* de[i][j] is the energy of the jth simulation in the ith Hamiltonian<o:p class=""></o:p></div>
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minus the energy of the jth simulation in the jth Hamiltonian */<o:p class=""></o:p></div>
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for (i = 0; i < re->nrepl; i++)<o:p class=""></o:p></div>
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{<o:p class=""></o:p></div>
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for (j = 0; j < re->nrepl; j++)<o:p class=""></o:p></div>
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{<o:p class=""></o:p></div>
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re->de[i][j] = 0;<o:p class=""></o:p></div>
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}<o:p class=""></o:p></div>
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for (i = 0; i < re->nrepl; i++)<o:p class=""></o:p></div>
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re->de[i][re->repl] = (enerd->enerpart_lambda[(int)re->q[ereLAMBDA][i]+1]-enerd->enerpart_lambda[0]);<o:p class=""></o:p></div>
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……<o:p class=""></o:p></div>
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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 class=""></o:p></div>
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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 class=""></o:p></div>
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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 class=""></o:p></div>
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if (debug)<o:p class=""></o:p></div>
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{<o:p class=""></o:p></div>
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fprintf(debug, "enerdiff lam %g: (%15s), non-linear %f linear %f*%f\n",<o:p class=""></o:p></div>
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fepvals->all_lambda[j][i], efpt_names[j],<o:p class=""></o:p></div>
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(enerd->enerpart_lambda[i+1] - enerd->enerpart_lambda[0]),<o:p class=""></o:p></div>
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dlam, enerd->dvdl_lin[j]);<o:p class=""></o:p></div>
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}<o:p class=""></o:p></div>
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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 class=""></o:p></div>
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Thanks,<o:p class=""></o:p></div>
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-ChrisM<o:p class=""></o:p></div>
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<p class="MsoNormal" style="margin: 0in 0in 12pt; font-size: 12pt; font-family: 'Times New Roman'; background-color: white; background-position: initial initial; background-repeat: initial initial;">
Mirabzadeh, Christopher <br class="">
Graduate Research Assistant/Physics Instructor<br class="">
Department of Physics<br class="">
University of Idaho<br class="">
Moscow, Id<br class="">
(509)339-5647<br class="">
<br class="">
<br class="">
<o:p class=""></o:p></p>
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<o:p class=""></o:p></div>
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