<div>Hi gmx-users, I am trying to build a CO2 topology. </div><div>Because CO2 is a triatomic linear molecule there </div><div>is a discontinuity in the potential for the angle of </div><div>180 degrees, so I must use virtual sites to circumvent </div>
<div>the problem. I have create my topology (gave below) </div><div>from arguments I read in the forum </div><div>(<a href="http://www.gromacs.org/pipermail/gmx-users/2003-February/004394.html">http://www.gromacs.org/pipermail/gmx-users/2003-February/004394.html</a>) </div>
<div>and for which I was a brief summary, also below. </div><div>But when I run the simulation I get the following error message. </div><div><br></div><div>"virtual site D1 (Res CO2) has non-zero mass 21.90158"</div>
<div><br></div><div>I understand and agree that the message, but what </div><div>I do not understand is, why the topology for CO2 gives </div><div>this error, while that for acetonitrile (below) does not. </div><div>Someboy could help me find the error?</div>
<div>Thanks</div><div>eef</div><div><br></div><div><br></div><div>*** My CO2 Topology ***</div><div>[ moleculetype ]</div><div>; name nrexcl</div><div>CO2 2</div><div><br></div><div>[ atoms ]</div><div>; nr type resnr residu atom cgnr charge<span class="Apple-tab-span" style="white-space:pre"> </span>mass</div>
<div>1 D1 1 CO2 D1 1 0.0000 21.90158</div><div>2 D2 1 CO2 D2 1 0.0000 21.90158</div><div>3 O 1 CO2 OC 1 -0.3256 0.00000 </div>
<div>4<span class="Apple-tab-span" style="white-space:pre"> </span>C 1 CO2 CO 1 0.6512 0.00000 </div><div>5 O 1 CO2 OC 1 -0.3256 0.00000 </div><div><br></div><div>
[ constraints ]</div><div>; ai aj funct b0</div><div>1 2<span class="Apple-tab-span" style="white-space:pre"> </span>1<span class="Apple-tab-span" style="white-space:pre"> </span> 0.2000</div><div><br>
</div><div>[ dummies2 ]</div><div>; ai aj ak funct a</div><div> 3 1 2 1 0.0170</div><div> 4 1 2 1 <span class="Apple-tab-span" style="white-space:pre"> </span>0.1000</div>
<div> 5 1 2 1<span class="Apple-tab-span" style="white-space:pre"> </span>0.2170<span class="Apple-tab-span" style="white-space:pre"> </span></div><div><br></div><div><br></div><div>[ exclusions ]</div><div>
3 4 5</div><div>4<span class="Apple-tab-span" style="white-space:pre"> </span>5<span class="Apple-tab-span" style="white-space:pre"> </span>3</div><div>5<span class="Apple-tab-span" style="white-space:pre"> </span>4<span class="Apple-tab-span" style="white-space:pre"> </span>3</div>
<div><br></div><div>;*** *** </div><div><br></div><div><br></div><div>*** From forum ***</div><div>;For acetonitrile</div><div>;The com of MeCN I get from:</div><div>;M = sum(mi)</div><div>;rcom = sum(mi*ri)/M</div><div>
;The inertia tensor of a linear molecule is:</div><div>; [Ia 0 0]</div><div>;I = [0 Ia 0] with Ia=sum(mi(ri-rcom)^2)</div><div>; [0 0 0]</div><div>;Now I have to choose to masses m1 and m2 with r1 and r2 relativ to the com:</div>
<div>;The distance R between m1 and m2 can be chosen freely:</div><div>;R = r1 - r2</div><div>;There are three conditions to be satisfied:</div><div>;M = m1 + m2</div><div>;m1*r1 + m2*r2 = 0</div><div>;m1*r1^2 + m2*r2^2 = Ia</div>
<div>;Using these 4 eqn I can calculate the four unknows.</div><div>;</div><div>;</div><div>;The correct Me-N-distance from the reference i cited is 0.263nm.</div><div>;The distance R between D1(m1) and D2(m2) is in priciple free to choose.</div>
<div>;only if you choose it shorter than r(Me-N) the quadratic equation</div><div>;you find for the first unknown paramter to define becomes undefined:</div><div>;</div><div>; M*R +- sqr(M^2R^2-4MIa)</div><div>;r1 = -----------------------</div>
<div>; 2M</div><div>;</div><div>;I got two solutions for r1. Calculating r2=r1-R will give you the</div><div>;negative of the other solution. I have chosen the solution</div><div>;that makes physical sense to me:</div>
<div>;</div><div>;D1--Me-------+-C--D2---N</div><div>; ^</div><div>; |</div><div>; com</div><div>;You have to consider that m(D1)<<m(D2). Hence the above config makes more</div>
<div>;sense than the other mathematical solution:</div><div>;</div><div>; Me-D2----+-C-------N-D1</div><div>;</div><div>;</div><div>*** ***</div><div><br></div><div><br></div><div>;*** Forum Acetonitrile Topology ***</div>
<div>[ atomtypes ]</div><div>;type mass charge ptype c6 c12</div><div>D1 9.49031 0.000 D 0.0 0.0</div><div>D2 31.56239 0.000 D 0.0 0.0</div>
<div>MeAN 0.00000 0.000 A 0.90571E-02 0.26212E-04 ; (*)</div><div> CAN 0.00000 0.000 A 0.51454E-02 0.12167E-04 ; (*)</div><div> NAN 0.00000 0.000 A 0.26955E-02 0.28943E-05 ; (*)</div>
<div><br></div><div>[ moleculetype ]</div><div>; name nrexcl</div><div>Acetonitril 2</div><div><br></div><div>[ atoms ]</div><div>; nr type resnr residu atom cgnr charge mass</div><div>1 D1 1 MeCN D1AN 1 0.000 9.49031</div>
<div>2 D2 1 MeCN D2AN 1 0.000 31.56239</div><div>3 MeAN 1 MeCN C3AN 1 0.206 0.00000</div><div>4 CAN 1 MeCN C4AN 1 0.247 0.00000</div>
<div>5 NAN 1 MeCN N5AN 1 -0.453 0.00000</div><div><br></div><div>[ constraints ]</div><div>; ai aj funct b0</div><div>1 2 1 0.26300</div><div><br></div><div>
[ dummies2 ]</div><div>; ai aj ak funct a</div><div> 3 1 2 1 0.2652197</div><div> 4 1 2 1 0.8203527</div><div> 5 1 2 1 1.2652197</div>
<div><br></div><div>[ exclusions ]</div><div>3 4 5</div><div>4 5 3</div><div>5 4 3</div><div><br></div><div>;(*) E.Guardia, Mol. Simul. 26, 2001, 2878;</div><div>;A rigid two mass system with the same mom. of inertia</div>
<div>;as MeCN is used to provide a linear molecule. Me, C and</div><div>;N are defined as dummies relativ to D1 and D2.</div><div>;---------------- eof -------------------</div><div>*** ***</div><div><br></div><div><br></div>
_______________________________________<br>Eudes Eterno Fileti<br>Centro de Ciências Naturais e Humanas<br>Universidade Federal do ABC<br>Rua Santa Adélia, 166 - Bloco B, Sala 1048<br>09210-170 Santo André - SP Brasil<br>
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