Hi,
> 1. In VMD, I loaded the prmtop file then followed by the AMBER restart
> (for
> *rst)* or AMBER coordinate (for *crd)* accordingly. For this point, I am
> checking again the options to open in VMD, something related to implicit
> solvent and periodic simulation.
Load type crd vs. crdbox is a likely culprit...
> 2. I wanted to unfold my protein using heating (from 0K to 400K) gradually
> in 50ps, then MD has been running for re-folding it (temp from 400K down
> to
> 300K and keep 300K for equilibration) in ~ 60ns (it is still running now).
> I want to detect the folding simulation, but because my protein is quite
> big
> (158 aa), and I think it is infeasible to fold it from scratch (from its
> sequence), so I started with a process of unfolding a homology model, and
> make it re-fold again.
This goes beyond technical help and into my personal scientific opinion,
but I do believe it unlikely that an unfolded protein will spontaneously
fold in 60 ns. If you unfold it completely first, it will not retain any
'memory' of the folded state and therefore not fold any quicker than a
random starting structure. Or, phrased differently, if after your
unfolding the protein *does* retain a preference to fold right back, your
unfolding was not complete.
> I hope my reasoning is not so wrong so far. As you said, it was NOT
> unfolded, so will you suggest me to increase the temperature to heat it up
> OR could you give me some suggestion to unfold it please?
if you go even higher in T, you may run into simulation stability problems
at some point. Your initial unfolding run is only 50ps! Simulating (much,
much) longer could help the unfolding process. Alternatively, adding
forces to pull e.g. the termini apart will force unfolding as well...
Please consider that what you are trying to do is not a standard
simulation by any means, by prepared to invest lots of brain and computer
power to get something worthwhile here...
Kind Regards,
Thomas
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Mon Sep 19 2011 - 04:30:03 PDT
