[gmx-users] Still model

Chi-cheng Chiu none0421 at gmail.com
Sun Apr 10 01:25:49 CEST 2011


Hi Yuguang,
Thanks for the input. For the AMBER vs GROMACS comparison, what GB model you
were using, OBC, HCT, or Still. Also, do you notice any source code
questions that I mentioned ?
Thanks

Regard,

Chi-cheng

On Fri, Apr 8, 2011 at 10:24 PM, Mu Yuguang (Dr) <YGMu at ntu.edu.sg> 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.
>
>
>
> Yuguang
>
>
>
>
>
> *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
>
> ------------------------------
> 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
>
> --
> 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
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110409/7434903d/attachment.html>


More information about the gromacs.org_gmx-users mailing list