Re: Temperature dependent unfolding..

From: Arun Krishnan (krishnan_at_ttck.keio.ac.jp)
Date: Wed Sep 05 2007 - 08:37:45 CDT

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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