[gmx-users] parts of protein unfolds during MD simulations

[Mark Abraham]

jayant james wrote:
> Hi!
> I have an issue with my protein modelling. I find that some of the helices
> (not all) have greatly unfolded during a 8ns distance restrained MD run. I
> am using the parameters below for the MD run. Is there any thing that can
> treat the system better than PME?

In general, no.

> title               =  Yo
> cpp                 =  /usr/bin/cpp
> define              = -DDISRES
> constraints         =  none
> ;constraint_algorithm =  lincs
> ;lincs_order         =  4
> integrator          =  md
> dt                  =  0.001    ; ps !
> nsteps              =  1000000  ; total 1.0ns.
> nstcomm             =  1
> nstxout             =  5000
> nstvout             =  5000
> nstfout             =  5000
> nstlog              =  5000
> nstenergy           =  500
> nstlist             =  10
> ns_type             =  grid
> rlist               =  1.0
> coulombtype         =  PME
> rcoulomb            =  1.0
> vdwtype             =  cut-off
> rvdw                =  1.4
> fourierspacing      = 0.12
> fourier_nx          = 0
> fourier_ny          = 0
> fourier_nz          = 0
> pme_order           = 4
> ewald_rtol          = 1e-5
> optimize_fft        = yes
> disre               =  simple
> disre_weighting     =  equal
> ; Berendsen temperature coupling is on in two groups
> Tcoupl              =  V-rescale
> tc-grps             =  tnc Non-Protein tnt NMR tni

Only an unusual system would be treated well by five different 
temperature coupling groups. Temperature coupling algorithms work well 
in conditions that resemble thermodynamic limits - large groups of atoms 
with homogeneous heat capacity.

Mark

> tau_t               =  0.1 0.1 0.1 0.1 0.1
> ref_t               =  300 300 300 300 300
> ; Energy monitoring
> energygrps          = Protein Non-Protein
> ;tnc Non-Protein tnt NMR tni
> ; Pressure coupling is not on
> Pcoupl              =  parrinello-rahman
> tau_p               =  0.5
> compressibility     =  4.5e-5
> ref_p               =  1.0
> ; Generate velocites is on at 300 K.
> gen_vel             =  yes
> gen_temp            =  300.0
> gen_seed            =  173529
> 
> 
> 
> 
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