From: Jerome Henin (jhenin_at_cmm.chem.upenn.edu)
Date: Wed May 21 2008 - 11:29:42 CDT
The NAMD tutorial will help you:
and of course the user's guide:
On Wed, May 21, 2008 at 9:16 AM, S.K. Ghosh <skg30_at_cam.ac.uk> wrote:
> Dear NAMD users,
> Thanks for your all yesterday's suggestions. As Axel pointed out that even 5
> picosec of simulation with organometallic contacts would need more than a
> month simulation, and my interest is of a few nanosecs, I would rather start
> with only biotin-streptavidin complex. The biotin will be fixed and force
> will be applied to streptavidin (similar to an AFM exp). From my reading of
> the tutorial this seems to be implementable in NAMD. I would appreciate your
> views on this.
> I have got the complex (PDB code: 1swe) from Preotein Data Bank. Could you
> please let me know where I could get the psf and parameter files from.
> This would be very helpful indeed.
> On May 20 2008, Axel Kohlmeyer wrote:
>> On Tue, 20 May 2008, S.K. Ghosh wrote:
>> SKG> Dear users,
>> dear sourav,
>> SKG> I am planning to set up the following simulation in NAMD. I would lke
>> to SKG> get your suggestion on whether this is feasible to do in NAMD. SKG>
>> SKG> I am trying to model the dynamics of biotin-streptavidin molecule where
>> SKG> biotin (thiolated) would remain attached to a Gold surface of a
>> resonator SKG> (QCM). So there would be a couple of layers of Au atoms, on
>> top of it would SKG> be a single layer of S atoms, on top of it Biotin, and
>> attached to it one
>> actually the structure of thiols on gold is not that trivial.
>> please see for example Mazzarello et al. PRL 98, 016102 (2007).
>> SKG> strand of Straptavidin. I would like to investigate the forces in the
>> SKG> biotin-streptavidin bond as well as the S-Biotin and S-Au bond. Giving
>> all SKG> the atoms an acceleration I would be interested to find out which
>> bond SKG> gives in first, calculating the binding energy.
>> please note that in typical classical force fields bonds are represented
>> by harmonic potentials, i.e. they cannot break
>> and are only realistic near the equilibrium distance.
>> you would have to use a different functional form. but even then
>> i doubt that a classical potential is sufficient to describe the
>> behavior. see for example Krueger et al., PRL 89, 186402 (2002)
>> and Konopka et al., JACS 126, 1203 (2004).
>> you would have to do a quite complicated and time consuming QM/MM
>> simulation, which would probably also need you to adjust
>> and existing QM/MM code to be able to handle a metallic surface system.
>> all qm/mm "bio"-capable codes i know (and i've seen quite a few over the
>> last years) assume a small, isolated QM system.
>> SKG> Is this possible to be set-up and run in NAMD? SKG> SKG> Is giving a
>> constant acceleration to all atoms feasible? Is it possible to
>> i'd say that the constant acceleration will be the least of your problems.
>> have you made a reality check? how fast on the atomic scale does your system
>> move in the experiment? what is the period of the vibrations?
>> p.s.: just to give you an estimate... a 5 picosecond DFT trajectory of 16
>> hexane thiols on a 4-layer gold slab takes about a full month running 24/7
>> on one rack of a bluegene/l (2048 cpus) (=1.5 mio cpu hours).
>> SKG> get the parameter files for Au-S, Biotin-S and Biotin-Streptavidin?
>> SKG> Your help would be precious in my work and would be much appreciated.
>> SKG> SKG> Thanks very much.
>> SKG> Sourav
>> SKG> SKG> SKG>
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