From: Arun Krishnan (krishnan_at_ttck.keio.ac.jp)
Date: Wed Sep 05 2007 - 10:56:56 CDT
Hi Viktor,
You can view the log files at:
http://www.iab.keio.ac.jp/~krishnan/downloads/equilibrate_520K.log
http://www.iab.keio.ac.jp/~krishnan/downloads/production_520K.log
Cheers,
Arun
On 9/6/07, Victor Ovchinnikov <ovchinnv_at_mit.edu> wrote:
>
> Could you post part of your output file for equilibration & production
> at 520 as well?
>
> Thanks
>
> On Wed, 2007-09-05 at 22:37 +0900, 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
> > b) heating to 300K:
> > http://www.iab.keio.ac.jp/~krishnan/downloads/heating.namd
> > c) equilibration @300K:
> > http://www.iab.keio.ac.jp/~krishnan/downloads/equilibrate_300K.namd
> > d) production @300K:
> > http://www.iab.keio.ac.jp/~krishnan/downloads/production_300K.namd
> > e) heating to 520K:
> > http://www.iab.keio.ac.jp/~krishnan/downloads/heating_to_520K.namd
> > f) equilibration @520K:
> > http://www.iab.keio.ac.jp/~krishnan/downloads/equilibrate_520K.namd
> > g) production @520K:
> > http://www.iab.keio.ac.jp/~krishnan/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> 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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> > Date: 5/24/2007 4:01 PM
> > >
> >
>
>
-- *********************************************** 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 **********************************************
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