From: Branko (bdrakuli_at_chem.bg.ac.rs)
Date: Mon Oct 10 2011 - 10:11:42 CDT
One additional connected question, to obtain more complete answer in
whole . I was used GBIS in NAMD 2.8 for implicit solvation in EtOH, to
this point (because of short alkyl chain in alcohol) lack of hydrophobic
term should not be a problem. But solvated (small organic molecules) are
hydrophobic in significant extent (and very soluble in EtOH in
reality). So if there is really lack of hydrophobic term in GBIS, as
implemented in NAMD, did I obtained reliable results?
On 10/10/2011 2:24 PM, Jérôme Hénin wrote:
> Hi everyone,
> I have just read the very interesting paper that describes how
> Generalized Born Implicit Solvent was parallelized in NAMD. A
> well-known limitation of GBIS is that it does not describe hydrophobic
> solvation or the hydrophobic effect in water. That effect is of course
> pretty important for protein conformation, and completely central to
> anything involving membranes. That's why some implementations of GBIS
> are augmented with empirical nonpolar solvation terms (e.g. ),
> which NAMD does not have so far , although it implements the method
> of Onufriev et al. who did use such a term in their work .
> Given these circumstances, what classes of problems is NAMD/GBIS
> well-suited for?
> Thanks for your input,
>  http://pubs.acs.org/doi/abs/10.1021/ct200563j
>  http://onlinelibrary.wiley.com/doi/10.1002/jcc.21813/abstract
>  http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/13710.html
>  http://onlinelibrary.wiley.com/doi/10.1002/prot.20033/full
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