From: Neema Salimi (nsalimi_at_msg.ucsf.edu)
Date: Wed Sep 05 2007 - 12:30:29 CDT
Well, too high a pressure and the protein won't have room to unfold
(I experienced this directly). Too low, I'm not so sure. It's
possible that if the pressure is too low (i.e. 1 bar), the protein-
water interactions won't be right as the box will be too big, but I
can't say for sure as I didn't directly test that. As for going with
a pressure of ~30 bars, I did that because the vapor pressure of
water at 500K is around 27 bars, so I wanted to be close to
conditions where water would actually be liquid.
On Sep 5, 2007, at 10:21 AM, Arun Krishnan wrote:
> Ahha... that makes sense..however.. are you sure that the higher
> pressure doesn't
> change the unfolding pathway? Any work been done on that? Or your
> experience?
>
> Cheers,
>
> Arun
>
> On 9/6/07, Neema Salimi <nsalimi_at_msg.ucsf.edu> wrote:
> I wonder if the pressure is an issue. I found it to be in some of my
> simulations, and after going with a pressure of ~30 bars, it worked
> fine (didn't try ubiquitin). I also did NVE simulations
> (equilibrated at NPT). Also, if I remember correctly, different
> groups have had different unfolding behavior for ubiquitin, so that
> may be something to look into.
>
> On Sep 5, 2007, at 8:37 AM, Peter Freddolino wrote:
>
> > 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
> >>>> -
> >>>>
> >>>
> >>
> >>
> ---------------------------------------------------------------------
> >> ---
> >>
> >>>>
> >>>> Internal Virus Database is out-of-date.
> >>>> Checked by AVG Free Edition.
> >>>> Version: 7.5.472 / Virus Database: 269.8.0/817 - Release Date:
> >>> 5/24/2007 4:01 PM
> >>>>
> >>>
> >>
> >>
> >>
> >
>
> Neema Salimi
> nsalimi_at_msg.ucsf.edu
>
> University of California-San Francisco
> Graduate Group in Biophysics
> Agard Lab
> http://msg.ucsf.edu/agard/
> Lab Phone: (415) 476-5143
>
>
>
>
> --
> ***********************************************
> Arun Krishnan, Ph.D,
> Assistant Professor,
> Institute for Advanced Biosciences,
> Keio University,
> Center Building,
> Tsuruoka, Yamagata 997-0035
> Japan
> Phone: +81 (0)235-29-0824
> Email: krishnan_at_ttck.keio.ac.jp
> URL: http://www.iab.keio.ac.jp/~krishnan
> **********************************************
Neema Salimi
nsalimi_at_msg.ucsf.edu
University of California-San Francisco
Graduate Group in Biophysics
Agard Lab
http://msg.ucsf.edu/agard/
Lab Phone: (415) 476-5143
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