From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Tue May 10 2011 - 15:57:58 CDT
you could also try the new implicit solvent model
On Tue, May 10, 2011 at 22:20, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>wrote:
> Hello Arun, if you freeze most of the protein, you're not gaining much,
> because you're still computing all the non-bonded interactions between the
> protein and the rest. Also, as you said, you still need to solvate the full
> protein with water, most of which would go to waste. Personally, I'd much
> rather leave the whole protein free to move, if you have it.
> Or, if you really need something "quick and dirty", I would suggest cutting
> away most of the protein altogether and keep only the binding pocket, which
> you can then solvate with a much smaller water box. Since this is just a
> fragment which could lose quickly its fold, to keep it in place you may use
> harmonic position restraints (keyword: constraints) rather than freezing
> (keyword: fixedAtoms).
> ---- ----
> Giacomo Fiorin - Postdoctoral Researcher
> ICMS - Institute for Computational Molecular Science - Temple University
> 1900 N 12 th Street, Philadelphia, PA 19122
> ---- ----
> On Sat, May 7, 2011 at 10:20 PM, Arun Kumar Subramanian <
> aksub007_at_gmail.com> wrote:
>> Hi NAMD'ers,
>> I am trying to simulate the interactions and conformational changes of a
>> part of substrate within just one binding site (may be i dont want protein
>> to be flexible) using NAMD.
>> But it is still going to take the same amount of computational intensity
>> (if not, atleast far higher than simulating just few amino acids) if I
>> freeze the whole protein and allow flexibility only in that region. Moreover
>> I need to put the protein in a box and fill it with water, that is going to
>> add more computational cost. Is freezing a good choice if I wish to do this
>> simulation in a desktop computer with fairly good processor. I just want to
>> model this in a quick and approximate way. I predict that it might need
>> around 1-2 days to simulate 1 ns of this protein fully solvated with tip3p
>> waters in 64 processors in a cluster. Any help or suggestions to accomplish
>> this will be appreciated.
>> ArunKumar. S.
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