[gmx-users] unfolding a protein

[Siavoush Dastmalchi]

Hi Justi,
 
Thanks for the comments. Yes, I am showing MD ~.mdp file and I know that my system is not neutral. I am not following the unfolding path and my intention by unfolding the protein is to get a conformation which I could regard it as one of the feasible unfolded conformations.
Do you think, not neutralizing the system will somehow prevent unfolding?
 
Cheers, Siavoush  

________________________________

From: gmx-users-bounces at gromacs.org on behalf of Justin A. Lemkul
Sent: Wed 2008/02/20 06:35 ب.ظ
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] unfolding a protein



Quoting Siavoush Dastmalchi <Dastmalchi.s at tbzmed.ac.ir>:

> Hi there,
>
>
>
> I want to unfold a protein (hen egg white lysozyme) which has got 4 disulfide
> bounds. I have tried 1 ns of MD at 400 K either in vacuum or hydrated form
> and it didn't unfold. I know it may need longer time, but it doesn't show any
> sign of even starting to unfold. I think I am restraining the protein in some
> way. Please see below the content of ~.mdp file that I use.

My guess is that 1 ns is far too short to see any signs of unfolding.
Typically, we think of protein folding on the microsecond - second timescale,
so even if you speed things along by running your simulation at higher
temperature, you should be running tens of nanoseconds, if not 100 or more.
Check the literature to see what other people consider a reasonable time scale.

Also, what have you done in terms of minimization and equilibration?  Are you
showing the production MD .mdp file?

As far as "thinking" you are restraining your protein, these are things you need
to be very sure of :-)  Your topology likely specifies #include "posre.itp" if
you include a "define" statement within your .mdp file (which I don't see), so
I doubt you are restraining your protein in any way.

>
>
>
> Would you please let me know how I could unfold a protein using an MD
> simulation?
>
> Do you think unfolding a water soluble protein in vacuum would be faster?

Maybe, but what would it prove?

As a side note, are you including counterions in your simulation?  I don't see
them incorporated into your tc-grps, so I'm wondering if you have an
electroneutral system.

-Justin

>
>
>
> Cheers, Siavoush
>
>
>
> cpp                      = /lib/cpp
> include                  = -I../top
> integrator               = md
> dt                       = 0.002
> nsteps                   = 500000
> nstxout                  = 1000
> nstvout                  = 1000
> nstlog                   = 100
> nstenergy                = 100
> nstxtcout                = 100
> xtc_grps                 = protein sol
> energygrps               = protein sol
> nstlist                  = 10
> ns_type                  = grid
> rlist                    = 0.8
> coulombtype              = cut-off
> rcoulomb                 = 1.4
> rvdw                     = 1.4
> pbc                      = xyz
> tcoupl                   = berendsen
> tc-grps                  = protein sol
> tau_t                    = 0.1 0.1
> ref_t                    = 400 400
> Pcoupl                   = berendsen
> Pcoupltype               = isotropic
> tau_p                    = 1.0
> compressibility          = 4.5e-5
> ref_p                    = 1.0
> gen_vel                  = yes
> gen_temp                 = 400
> gen_seed                 = 173529
> constraints              = all-bonds
>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>



========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

========================================
_______________________________________________
gmx-users mailing list    gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php


-------------- next part --------------
A non-text attachment was scrubbed...
Name: winmail.dat
Type: application/ms-tnef
Size: 10160 bytes
Desc: not available
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080220/03813fd1/attachment.bin>