[gmx-users] Still model

Mark Abraham Mark.Abraham at anu.edu.au
Sun Apr 10 01:53:50 CEST 2011

On 9/04/2011 1:24 PM, Mu Yuguang (Dr) wrote:
> Dear Chi-Xheng,
> We have tried GB module in gromacs, but unfortunately we found 
> something wrong with it.
> What we found is that the results got from gromacs were quite 
> different from those obtained from AMBER codes.
> We did not check in details why.

I also have tried to compare some polyalanine implicit-solvation REMD 
with published AMBER results. I could not get agreement, however I noted 
that in a follow-up paper by the same authors using a higher AMBER 
version, they implied that they didn't get agreement with their earlier 
work, either. So perhaps there was an AMBER problem, or an AMBER-user 
problem. I can supply some details if useful.

> *From:*gmx-users-bounces at gromacs.org 
> [mailto:gmx-users-bounces at gromacs.org] *On Behalf Of *Chi-cheng Chiu
> *Sent:* Saturday, April 09, 2011 8:33 AM
> *To:* gmx-users at gromacs.org
> *Subject:* [gmx-users] Still model
> Hi all,
> I looked at source code in /src/mdlib/genborn.c and have two questions 
> regarding the Still implicit solvent model.
> 1.  in the function calc_gb_chainrule(), only Still model have extra 
> factor of 2 apply on dvda, which I don't know why.
> 2. in calc_gb_rad_still(), does dccf miss a factor of 2?  ( hope I did 
> my math correct....)
> Thanks in advance!
> Regard,
> Chi-xheng
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