Hi! I know about this difference. The only reason for it is that, when I first started with this I used Tinker as a reference implementation, which has the 6-th power in the code.
The differences should be small, though. The non-polar part only amounts to a few percent of the total force anyway. Cheers /Per 28 mar 2011 kl. 21:24 skrev Chi-cheng Chiu <none0...@gmail.com>: > 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 > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
