Re: Temperature dependent unfolding..

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Sep 05 2007 - 10:37:32 CDT

Hi Arun,
you might just want to start by looking at the box volume (from the xst
file), and how it varies with temperature. To get the water density, you
need to take those box volumes and subtract the protein volume (I
believe you can get this using MSMS, or from the server at
http://molbio.info.nih.gov/structbio/basic.html). This should let you
calculate the water density fairly easily. Large volume fluctuations in
an NPT md simulation can do odd things to the dynamics, which is why I'm
curious whether the volume varied as much in your case as it did in the
paper you cited.
Peter

Arun Krishnan wrote:
> 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
> <mailto: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>
> > < 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>
> > <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>
> >
> <http://www.iab.keio.ac.jp/%7Ekrishnan/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>
> > <
> 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>
> >
> <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>
> >
> <http://www.iab.keio.ac.jp/%7Ekrishnan/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>
> > <
> 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>
> > <mailto: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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