<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Hello<div><br></div><div><div>[ atomtypes ]</div><div>; type mass charge ptype c6 c12</div><div> CH3 15.035 0.000 A 9.0638e-3 2.5206e-5</div><div> CH2 14.027 0.000 A 5.8108e-3 2.2071e-5</div><div> CS2 14.027 0.000 A 5.8108e-3 2.2071e-5</div><div> OS 15.999 0.000 A 8.8147e-4 4.2477e-7 </div><div> OA 15.999
0.000 A 2.3465e-3 1.7802e-6</div><div> HO 1.008 0.000 A 0.0000e00 0.0000e00 </div></div><div><br></div><div>at atomtypes i can give c6 and c12 values and gromacs will generate the c6ij and c12ij values from the formulas i have chosen with selecting combination rule Am i right????</div><div><br></div><div>in my case i gave c6 and c12 as c6i=4*ei*ói^6 and c12i=4*ei*ói^12 and i chose combination rule 1. so gromacs will generate the c6ij and c12ij as c6ij=sqrt(C6iC6j) and c12ij=sqrt(c6i*c12j)</div><meta http-equiv="content-type" content="text/html; charset=utf-8"><div><br></div><div>So if in my topology I put [nonbond_params] what happens then? the values from [nonbond_params] c6 and c12 are being replaced by the values gromacs finds from the
equations???</div><div><br></div><div>for example</div><div><br></div><div>if i have </div><div><br></div><div><meta http-equiv="content-type" content="text/html; charset=utf-8">[nonbond_params] </div><div><br></div><div>CH3 CH3 5e-3 6e-5</div><div><br></div><div>and gromacs calculates from the [atomtypes] are different lets say (i didnt do the calculation it is an assumption value) 3e-2 and 3e-5 which values gromacs accepts?</div><div>i have read the manual but it isnd clear how this works. </div><div><br></div><div>please someone enlighten me.</div><div><br></div><div>thanks</div><meta http-equiv="content-type" content="text/html; charset=utf-8"><meta http-equiv="content-type" content="text/html; charset=utf-8"></td></tr></table><br>