[gmx-users] Still model

[Chi-cheng Chiu]

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
>
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