Re: Temperature dependent unfolding..

From: Monika Sharma (mon_sharma_at_research.iiit.ac.in)
Date: Wed Sep 05 2007 - 04:00:51 CDT

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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