<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Hello <div><br></div><div>I have sent several emails and i am sorry. It is my last attempt to finish this simulation.</div><div>The molecule i have is C-C-C-C-C-C-O-C-C-O-C-C-O-H or C10H1O3. (ciej molecule)</div><div><br></div><div>I dont use gromacs libraries</div><div>the files i use are attached to the email in which i have descriped step by step the forcefield i use. </div><div>as you can see in [pairs] i have an extra non Lj 1-4 pair. i did it because the model i use has a potential between atom 10 and 14 ether oxygen and alchohol hydrogen interaction. It is described in the paper as a repulsive energy between these two atoms. and it has a formula:</div><div><br></div><div>Erepulsive = 3.325789e-7/r^12</div><div><br></div><div>the only way to import in gromacs i think is this:</div><div><br></div><div><div>[ pairs ]</div><div>; ai aj
funct </div><div>10 14 2 0 0 0 0 3.325789e-7</div></div><div><br></div><div>it is an intra-molecular only interaction. so i couldnt think another way to do it except this. as you can see i have several zeros for the charges, C6=o and C12 = 3.325789e-7 fidgeQQ=0 for this case</div><div><br></div><div>the problem is i get positive total energy. i did this sim for only one molecule just to see what is wrong and i think that coulomb (SR) are wrong for sure.</div><div><br></div><div>so i want </div><div><br></div><div>coulomb 1-4 /2 !thats why i put fudgeQQ = 0.5</div><div><br></div><div>the values i get at the step 0 are</div><div><br></div><div><div>Energies (kJ/mol)</div><div> Angle Proper Dih. LJ-14 Coulomb-14 LJ (SR)</div><div> 2.30340e+03 1.08417e+00
3.16570e+00 8.79204e+04 -2.54164e+03</div><div> Disper. corr. Coulomb (SR) Coul. recip. Potential Kinetic En.</div><div> -2.51250e+00 -4.81042e+04 -2.84931e+04 1.10867e+04 1.84852e+04</div><div> Total Energy Temperature Pressure (bar) Cons. rmsd ()</div><div> 2.95719e+04 2.99528e+02 -3.03583e+02 3.13477e-06</div></div><div><br></div><div>tell me please how is this possible</div><div><br></div><div>thanks in advance and i am sorry once again</div><div><br></div><meta http-equiv="content-type" content="text/html; charset=utf-8"></td></tr></table><br>