[gmx-users] implicit solvent model: formulation of non-polar free energy

Per Larsson per.larsson at sbc.su.se
Mon Mar 28 22:09:06 CEST 2011


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.


28 mar 2011 kl. 21:24 skrev Chi-cheng Chiu <none0421 at 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 at 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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

More information about the gromacs.org_gmx-users mailing list