Hi everyone,<div>I am going through the source code for the GB calculation part of gromacs, and found the following code in "src/mdlib/genborn.c" :</div><div>in the function "real calc_gb_nonpolar()"</div>
<div><div><br></div><div>rai = top->atomtypes.gb_radius[md->typeA[ai]];</div><div>rbi_inv = fr->invsqrta[ai];</div><div>rbi_inv2 = rbi_inv * rbi_inv;</div><div>tmp = (rai*rbi_inv2)*(rai*rbi_inv2);</div>
<div>tmp = tmp*tmp*tmp;</div><div>e = factor*term*(rai+probe)*(rai+probe)*tmp;</div><div>dvda[ai] = dvda[ai] - 6*e*rbi_inv2; </div><div>es = es + e;</div></div><div><br></div><div>so from this source code, energy seems to be (rai+probe)^2 * (rai/rbi)^6</div>
<div>where rbi is the born radius, rai is the atom radius, and probe is 0.14 nm.</div><div>I checked the reference Schaefer et al. JMB 284(3):835–848, 1998 which is mentioned in the manual.</div><div>It seems the reference used (rai+probe)^2 * (rai/rbi) </div>
<div>where (rai/rbi) term don't have power of 6 and disagree with the source code.</div><div>Is there a reason using power 6?</div><div><br></div><div>Chi-cheng</div><div><br></div>