From: Arun Krishnan (krishnan_at_ttck.keio.ac.jp)
Date: Thu Sep 06 2007 - 20:09:46 CDT
Hi Neema,
When you did the simulation at ~30 bars, did you do that for only the
production run at 500K or for the heating/equilibration and production runs?
Thanks,
Arun
On 9/6/07, Neema Salimi <nsalimi_at_msg.ucsf.edu> wrote:
>
> 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/
> > <http://www.iab.keio.ac.jp/%7Ekrishnan/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
>
>
-- *********************************************** 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 **********************************************
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:45:13 CST