Justin already answered your questions. In short: make a DSSP map in order
to prove that secondary structure is indeed being lost. Visual inspection
is not sufficient (and most likely plain wrong). The RMSD and Rg will
naturally fluctuate. Unless the fluctuations are of too high magnitude or
irreversible (denaturation), there may be no problem at all.
On Fri, Sep 16, 2016 at 12:37 PM, soumadwip ghosh <soumadwipgh...@gmail.com>
> ---------- Forwarded message ----------
> From: soumadwip ghosh <soumadwipgh...@gmail.com>
> Date: Thu, Sep 15, 2016 at 9:16 PM
> Subject: protein getting unfolded in SPC/E water
> To: "gromacs.org_gmx-users" <firstname.lastname@example.org>
> I am simulating Lysozyme in pure SPC/E water for 200 ns. I am
> using OPLS-AA force field for my work. In pure water the protein looses
> some of its helices. As for example in the final md.gro file the number of
> alpha helices observed are 2 while in the beginning 4 were observed in VMD.
> The corresponding C-alpha RMSD and radius of gyration are also fluctuating.
> Could anyone help me understand what's going on?
> I am pasting the snippets of my topology and the md.mdp files.
> ; Include water topology
> #include "oplsaa.ff/spce.itp"
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ; i funct fcx fcy fcz
> 1 1 1000 1000 1000
> ; Include topology for ions
> #include "oplsaa.ff/ions.itp"
> [ system ]
> ; Name
> Protein in water
> [ molecules ]
> ; Compound #mols
> Protein_chain_A 1
> SOL 11071
> CL 9
> Here is the md.mdp one
> constraints = all-bonds ; all bonds (even heavy atom-H bonds)
> lincs_iter = 1 ; accuracy of LINCS
> lincs_order = 4 ; also related to accuracy
> ; Neighborsearching
> ns_type = grid ; search neighboring grid cells
> nstlist = 5 ; 10 fs
> rlist = 1.0 ; short-range neighborlist cutoff (in nm)
> rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
> rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
> ; Electrostatics
> coulombtype = PME ; Particle Mesh Ewald for long-range
> pme_order = 4 ; cubic interpolation
> fourierspacing = 0.16 ; grid spacing for FFT
> ; Temperature coupling is on
> tcoupl = V-rescale ; modified Berendsen thermostat
> tc-grps = SYSTEM ; two coupling groups - more accurate
> tau_t = 0.1 ; time constant, in ps
> ref_t = 310 ; reference temperature, one for each
> group, in K
> ; Pressure coupling is on
> pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT
> pcoupltype = isotropic ; uniform scaling of box vectors
> tau_p = 2.0 ; time constant, in ps
> ref_p = 1.0 ; reference pressure, in bar
> compressibility = 4.5e-5 ; isothermal compressibility of water,
> ; Periodic boundary conditions
> pbc = xyz ; 3-D PBC
> ; Dispersion correction
> DispCorr = EnerPres ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel = no ; Velocity generation is off
> energygrps = protein SOL
> I am quite sure that the system is well equilibrated.
> Here is the part of md.edr file
> Back Off! I just backed up energy.xvg to ./#energy.xvg.2#
> Last energy frame read 75000 time 150000.000
> Statistics over 75000001 steps [ 0.0000 through 150000.0000 ps ], 4 data
> All statistics are over 15000001 points
> Energy Average Err.Est. RMSD Tot-Drift
> Temperature 310.004 0.0015 1.64028 0.000388793 (K)
> Pressure 1.04308 0.00049 143.118 0.00201836 (bar)
> Volume 351.008 0.0063 0.835859 0.0314951
> Density 1012.78 0.018 2.41171 -0.0908186
> What might go wrong?
> Thanks for your time in advance.
> Soumadwip Ghosh
> Senior Research Fellow
> Indian Institute of Technology Bombay
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