From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Wed Feb 15 2012 - 15:45:54 CST
Great! Thanks. Gromacs has it, too, but I want to stay with NAMD for
several reasons.
I wonder whether there is a way to directly access the energy function of
NAMD so that I could use it as part of a Monte Carlo algorithm.
Thanks,
Gianluca
On Wed, 15 Feb 2012, David Tanner wrote:
> Not yet; it may be available in March or April.
>
> Thank you,
> David E. Tanner
>
> On Fri, Jan 20, 2012 at 6:41 PM, Gianluca Interlandi
> <gianluca_at_u.washington.edu> wrote:
>> Dear NAMD developers,
>>
>> I am just curious to know whether the SASA-proportional hydrophobic energy
>> term for implicit solvent simulations is available in one of the nightly
>> builds of NAMD.
>>
>> Thanks!
>>
>> Gianluca
>>
>>
>> On Thu, 13 Oct 2011, David Tanner wrote:
>>
>>> NAMD Implicit Solvent users,
>>> Though NAMD's implementation of implicit solvent does not currently
>>> include a
>>> SASA-proportional hydrophobic energy term, I believe one will be available
>>> early 2012.
>>>
>>> ...
>>>
>>>
>>> Thank you,
>>> David E. Tanner
>>>
>>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>>> David E. Tanner
>>> Theoretical and Computational Biophysics Group
>>> 3159 Beckman Institute
>>> University of Illinois at Urbana-Champaign
>>> 405 N. Mathews
>>> Urbana, IL 61801
>>> http://www.linkedin.com/in/davidetanner
>>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>>>
>>>
>>>
>>>
>>>
>>> On Mon, Oct 10, 2011 at 10:11 AM, Branko <bdrakuli_at_chem.bg.ac.rs> wrote:
>>> 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?
>>> Thanks
>>>
>>> Branko
>>>
>>>
>>>
>>>
>>> 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.[1] 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. [2]),
>>> which NAMD does not have so far [3], although it implements the method
>>> of Onufriev et al. who did use such a term in their work [4].
>>>
>>> Given these circumstances, what classes of problems is NAMD/GBIS
>>> well-suited for?
>>>
>>> Thanks for your input,
>>> Jerome
>>>
>>>
>>> [1] http://pubs.acs.org/doi/abs/10.1021/ct200563j
>>> [2] http://onlinelibrary.wiley.com/doi/10.1002/jcc.21813/abstract
>>> [3] http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/13710.html
>>> [4] http://onlinelibrary.wiley.com/doi/10.1002/prot.20033/full
>>>
>>>
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>>>
>>>
>>>
>>
>> -----------------------------------------------------
>> Gianluca Interlandi, PhD gianluca_at_u.washington.edu
>> +1 (206) 685 4435
>> http://artemide.bioeng.washington.edu/
>>
>> Postdoc at the Department of Bioengineering
>> at the University of Washington, Seattle WA U.S.A.
>> -----------------------------------------------------
>
-----------------------------------------------------
Gianluca Interlandi, PhD gianluca_at_u.washington.edu
+1 (206) 685 4435
http://artemide.bioeng.washington.edu/
Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
-----------------------------------------------------
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