---------- 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" <gromacs.org_gmx-users@maillist.sys.kth.se>
Hello, 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 #endif ; 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) constrained 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 electrostatics 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, bar^-1 ; 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 sets 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 (nm^3) Density 1012.78 0.018 2.41171 -0.0908186 (kg/m^3) What might go wrong? Thanks for your time in advance. Soumadwip Ghosh Senior Research Fellow Indian Institute of Technology Bombay India -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.