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