<div style='background-color:#ffffff;'><style>P {font-size:10pt;font-family:±¼¸²,Gulim,Helvetica,serif;margin-top:7px;margin-bottom:0px;}</style><P>Dear GROMACS users,</P>
<P> </P>
<P>I'm wondering how can I correctly describe H-H radial distribution function of heavy water.</P>
<P>Please check atteched file HH_rdf.PNG which is a calculated result of H-H radial distribution from my simulation.</P>
<P>The first peak is due to the intramolecular interaction of water molecules.</P>
<P>It shows almolst 7 at 0.13 nm but when comparing this result with an experimental data, the experimental data shows just almost 2 at the first peak.</P>
<P>I have tried many times of simulations but i couldn't find why this huge difference is caused.</P>
<P>I used tip4p/2005f water model and used potential is atteched below.</P>
<P> </P>
<P>[ defaults ]<BR>; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ<BR>1 3 yes 0.5 0.5</P>
<P> </P>
<P>[ moleculetype ]<BR>; molname nrexcl<BR>SOL 2</P>
<P> </P>
<P>[ atoms ]<BR>; id at type res nr residu name at name cg nr charge<BR>1 opls_113 1 SOL OW 1 0.0<BR>2 opls_114 1 SOL HW1 1 0.5564<BR>3 opls_114 1 SOL HW2 1 0.5564<BR>4 opls_115 1 SOL MW 1 -1.1128</P>
<P> </P>
<P>;[nonbond_params]<BR>; i j funct q V W<BR>;1 2 1 0.5564 3.16440e-01 7.74907e-01 <BR>;1 3 1 0.5564 3.16440e-01 7.74907e-01</P>
<P><BR>#ifndef FLEXIBLE<BR>[ settles ]<BR>; OW funct doh dhh<BR>1 1 0.09664 0.15555</P>
<P>#else</P>
<P>[ bonds ]<BR>; i j funct length D beta<BR>1 2 3 0.09419 432.581 22.87 ; For TIP4P/2005f Water b0, D, beta <BR>1 3 3 0.09419 432.581 22.87 ; For TIP4P/2005f Water b0, D, beta <BR> <BR>[ angles ]<BR>; i j k funct angle force.c.<BR>2 1 3 1 107.4 367.81 <BR>#endif</P>
<P>[ exclusions ]<BR>1 2 3 4<BR>2 1 3 4<BR>3 1 2 4<BR>4 1 2 3</P>
<P> </P>
<P>; The position of the virtual site is computed as follows:<BR>;<BR>; const = distance (OD) / [ cos (angle(DOH)) * distance (OH) ]<BR>; 0.015 nm / [ cos (52.26 deg) * 0.09572 nm ]</P>
<P>; Vsite pos x4 = x1 + a*(x2-x1) + b*(x3-x1)</P>
<P>[ virtual_sites3 ]<BR>; Vsite from funct a b<BR>4 1 2 3 1 0.13288 0.13288</P>
<P><BR>I used -DFLEXIBLE option and energy minimization, NVT, NPT equlibration and NVE production run.</P>
<P>If someone would find some wrong things, please let me know.</P>
<P> </P>
<P>Thank you.</P>
<P>Haelee Hyun<BR></P>
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