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.
Mark
*From:*gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] *On Behalf Of *Chi-cheng Chiu
*Sent:* Saturday, April 09, 2011 8:33 AM
*To:* gmx-users@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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