From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Sep 05 2007 - 09:06:31 CDT
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
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.
Arun Krishnan wrote:
> Hi Monika,
> I have uploaded all my config files to my website. You can get them
> from here:
> a) energy minimization:
> b) heating to 300K:
> c) equilibration @300K:
> d) production @300K:
> e) heating to 520K:
> f) equilibration @520K:
> g) production @520K:
> 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
> Do let me know if you see anything wrong.
> Thanks in advance.
> On 9/5/07, *Monika Sharma* <mon_sharma_at_research.iiit.ac.in
> <mailto:mon_sharma_at_research.iiit.ac.in>> wrote:
> 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.
> 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
> > 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:
> > 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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