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Hello. Thanks!
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<div class="">I actually want to do calculations between lambda steps inside of GROMACS code, before the end of the simulation.</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="">
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<div class="">On Apr 20, 2017, at 4:14 PM, Michael R Shirts <<a href="mailto:Michael.Shirts@Colorado.EDU" class="">Michael.Shirts@Colorado.EDU</a>> wrote:</div>
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<span style="font-size: 11pt; font-family: Calibri;" class="">Hi, Chris-<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="">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: rgb(149, 79, 114); text-decoration: underline;" class="">https://github.com/MobleyLab/alchemical-analysis/</a><span class="Apple-converted-space"> </span>scripts
for how this information is used.<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="">The ROUTE to getting the values right is rather complicated for a number of reasons. So before answering in more detail-<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=""><span class="">1.<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><span style="font-size: 11pt; font-family: Calibri;" class="">If
you want to just USE this information, it’s all output by GROMACS already.<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri;" class=""><span class="">2.<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><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?<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="">~~~~~~~~~~~~~~~~<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: rgb(149, 79, 114); text-decoration: underline;" class=""><span style="color: blue;" class="">michael.shirts@colorado.edu</span></a><o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri;" class=""><a href="http://www.colorado.edu/lab/shirtsgroup/" style="color: rgb(149, 79, 114); text-decoration: underline;" class=""><span style="color: blue; text-decoration: none;" class="">http://www.colorado.edu/lab/shirtsgroup/</span></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" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">gromacs.org_gmx-developers-bounces@maillist.sys.kth.se</a>>
on behalf of "Mirabzadeh, Christopher (<a href="mailto:mira2978@vandals.uidaho.edu" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">mira2978@vandals.uidaho.edu</a>)" <<a href="mailto:mira2978@vandals.uidaho.edu" style="color: rgb(149, 79, 114); text-decoration: underline;" 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" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">gmx-developers@gromacs.org</a>" <<a href="mailto:gmx-developers@gromacs.org" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">gmx-developers@gromacs.org</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: rgb(149, 79, 114); text-decoration: underline;" class="">gmx-developers@gromacs.org</a>" <<a href="mailto:gmx-developers@gromacs.org" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">gmx-developers@gromacs.org</a>><br class="">
<b class="">Subject:<span class="Apple-converted-space"> </span></b>[gmx-developers] energy difference for lambda in free energy calculations<o:p class=""></o:p></span></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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<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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}<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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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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<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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<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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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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