Re: Temperature dependent unfolding..

From: Arun Krishnan (krishnan_at_ttck.keio.ac.jp)
Date: Wed Sep 05 2007 - 09:26:26 CDT

Hi Peter,

I did check the temperature.. and it was stable at around 518K... also...
interestingly, after my equilibration run
at 300K, I noticed that the temperature stabilized at around 298K... would
that lead to any problems?

Also, how do I find out the water density? Can you explain that in short
please?

Thanks,

Arun

On 9/5/07, Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
>
> Hi Arun,
> have you, for example, plotted the temperature output from this run to
> verify that the temperature is stable and at 520K? I ask partly because
> I don't recall how namd interprets the string "520K" as a floating point
> number; normally one would simply give the value in Kelvin, but omit the
> unit.
>
> Also, what average volume (or water density) do you see at 520K compared
> to the 300 K equilibration? It looks like some very large fluctuations
> were observed in the paper you cited, but they do not make it clear what
> method they used for pressure control.
>
> Best,
> Peter
>
> Arun Krishnan wrote:
> > Hi Monika,
> >
> > I have uploaded all my config files to my website. You can get them
> > from here:
> >
> > a) energy minimization:
> > http://www.iab.keio.ac.jp/~krishnan/downloads/min.namd
> > <http://www.iab.keio.ac.jp/%7Ekrishnan/downloads/min.namd>
> > b) heating to 300K:
> > http://www.iab.keio.ac.jp/~krishnan/downloads/heating.namd
> > <http://www.iab.keio.ac.jp/%7Ekrishnan/downloads/heating.namd>
> > c) equilibration @300K:
> > http://www.iab.keio.ac.jp/~krishnan/downloads/equilibrate_300K.namd
> > <http://www.iab.keio.ac.jp/%7Ekrishnan/downloads/equilibrate_300K.namd>
> > d) production @300K:
> > http://www.iab.keio.ac.jp/~krishnan/downloads/production_300K.namd
> > <http://www.iab.keio.ac.jp/%7Ekrishnan/downloads/production_300K.namd>
> > e) heating to 520K:
> > http://www.iab.keio.ac.jp/~krishnan/downloads/heating_to_520K.namd
> > <http://www.iab.keio.ac.jp/%7Ekrishnan/downloads/heating_to_520K.namd>
> > f) equilibration @520K:
> > http://www.iab.keio.ac.jp/~krishnan/downloads/equilibrate_520K.namd
> > <http://www.iab.keio.ac.jp/%7Ekrishnan/downloads/equilibrate_520K.namd>
> > g) production @520K:
> > http://www.iab.keio.ac.jp/~krishnan/downloads/production_520K.namd
> > <http://www.iab.keio.ac.jp/%7Ekrishnan/downloads/production_520K.namd>
> >
> > I ran these under NPT.. so some of the comments in the files might not
> > make sense. (These were put in when I was initially doing an NVT
> > ensemble).
> >
> > Do let me know if you see anything wrong.
> >
> > Thanks in advance.
> >
> > Cheers,
> >
> > Arun
> >
> > On 9/5/07, *Monika Sharma* <mon_sharma_at_research.iiit.ac.in
> > <mailto:mon_sharma_at_research.iiit.ac.in>> wrote:
> >
> > hii!!
> > can you just write your conf file here the last part of the
> run?There
> > might be some problem in going from 300K to 500K.
> > regards,
> > monika
> > Arun Krishnan wrote:
> > > Dear NAMD list users,
> > >
> > > I have been trying to carry out unfolding simulations of
> > Ubqiuitin. I
> > > use the top_all22_prot.inp and par_all22_prot.inp topology and
> > > parameter files.
> > > I did the following steps:
> > >
> > > a) Energy minimization
> > > b) Heating to 300K
> > > c) Equilibration for 50ps NPT
> > > d) Production run @300K for 1ns. NPT
> > > e) Heating to 500K
> > > f) Equilibration for 50ps NPT
> > > g Production run @500K for 12ns NPT
> > >
> > > Very surprisingly, I don't see the RMSD values changing (with
> > respect
> > > to the final equilibrated frame at 300K) by greater than 4-5
> > > Angstroms. This is very weird. There is a paper in Physical
> > Review E,
> > > 72, 051928, 2005 "Unfolding dynamics of the protein ubiquitin:
> > Insight
> > > from simulation" where they achieved drastic unfolding within 1ns
> > > for ubiquitin at 520K. I followed what they did and tried at
> > 520K too.
> > >
> > > I have used NPT throughout.. but I also used NVT and NVE
> ensembles..
> > > and in all cases it seems to be very stable. Does anyone have any
> > > pointers to what I might be doing wrong?
> > >
> > > Thanks in Advance,
> > >
> > > Arun
> > > -
> > >
> >
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> >
>

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