[gmx-users] unfolding a protein

[Xavier Periole]

On Thu, 21 Feb 2008 14:54:35 +0530 (IST)
  mon_sharma at research.iiit.ac.in wrote:
> On Wed, 20 Feb 2008, Siavoush Dastmalchi wrote:
> Hii!!
> The time scale you have chosen is very less to see unfolding in proteins of 
>moderate length, because in such a short time u might be able to see just 
>local disturbances only, even at temperature of 400K. You need to increase 
>the production run time, atleast go for 3n. And you might not need constrains 
>of all-bonds to put.

one paper that might be interest:

Wang and Wade, JCTC-2007 3:1476

> Cheers,
> Monika
> 
>> 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.
>>
>>
>>
>> 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?
>>
>>
>>
>> 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
>>
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> 
> 
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-----------------------------------------------------
XAvier Periole - PhD

NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
-----------------------------------------------------