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<div>Dear Board,</div>
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<div>I have done this with a steered MD, using covarience, etc...in the end there are nice delG and H,S line graphs...the only argument I have heard however is when doing the subtraction the third curve always gives the correct repective energy change, but the delG line graph may not always represent the energy "path" correctly as there becomes a large amount of overlap in energy changes between other groups not in the index grp used (ions, h2o, long range effects lowering conformational states such as a 3 water bridge to another protein....) ...only making it much more cumbersome, or making the delS or H have much higher STDV or total error that can for a biochemist looking at say a small ligand binding energy squirm (delG say of 20 kCal/mol but STDV or error at +/- 10 kCal/mol where say a protein protein or DNA interaction may have dips and wells in the 100's of kCal/mol range so not quite as problematic...all assuming one is not using a QQMM where the errors go down one or two orders ofmagnitude)...theH/S pathways though can be informative especially for biologist looking at macromolecules...I would be interested in opinions/thoughts on these differences though...</div>
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<div>Stephan Watkins</div>
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<div style="margin:0 0 10px 0;"><b>Gesendet:</b> Montag, 17. März 2014 um 09:26 Uhr<br/>
<b>Von:</b> "David van der Spoel" <spoel@xray.bmc.uu.se><br/>
<b>An:</b> gmx-users@gromacs.org<br/>
<b>Betreff:</b> Re: [gmx-users] binding delta G, H and S for ion-protein</div>
<div name="quoted-content">On 2014-03-16 19:05, Andrew Bostick wrote:<br/>
> Dear Justin<br/>
><br/>
> Thanks for your answer.<br/>
><br/>
> All of methods you mentioned ( PMF, TI, FEP, BAR) are used for calculating<br/>
> free energy (G). In addition to free energy (G), I want to calculate<br/>
> enthalpy (H) and entropy (S).<br/>
><br/>
> Are you sure can I use above methods for calculating both of enthalpy (H)<br/>
> and entropy (S)?<br/>
><br/>
You can compute H and S by doing a temperature series and use the Van 't<br/>
Hoff equation. A bit expensive though. Sometimes for well-defined<br/>
systems if you do a PMF you can subtract the enthalpy coming from the<br/>
simulation to obtain the entropy. See e.g.<br/>
PNAS 108 pp. 6838-6842 (2011)<br/>
><br/>
> Best wishes<br/>
><br/>
<br/>
<br/>
--<br/>
David van der Spoel, Ph.D., Professor of Biology<br/>
Dept. of Cell & Molec. Biol., Uppsala University.<br/>
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.<br/>
spoel@xray.bmc.uu.se <a href="http://folding.bmc.uu.se" target="_blank">http://folding.bmc.uu.se</a><br/>
--<br/>
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