[gmx-users] Still model

Mu Yuguang (Dr) YGMu at ntu.edu.sg
Sat Apr 9 05:24:41 CEST 2011

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.


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!



CONFIDENTIALITY: This email is intended solely for the person(s) named and may be confidential and/or privileged. If you are not the intended recipient, please delete it, notify us and do not copy, use, or disclose its content. Thank you.

Towards A Sustainable Earth: Print Only When Necessary
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110409/5db2156f/attachment.html>

More information about the gromacs.org_gmx-users mailing list