Try a smaller integration timestep while you equilibrate. Set nstxout = 1 and look closely at the region that starts to break. Try without constraints. Alternatively, simplify/change the problem by (say) stripping all the crystal waters before adding, or solvating only one copy of the protein (to diagnose topology issues).
Mark ----- Original Message ----- From: Itamar Kass <[email protected]> Date: Monday, October 18, 2010 11:14 Subject: [gmx-users] Problems when simulating a protein in its crystal matrix. To: Discussion list for GROMACS users <[email protected]> ----------------------------------------------------------- | @font-face { font-family: "Courier New"; }...@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman"; }div.Section1 { page: Section1; } > Hi All, I wish to simulate a protein in its crystal form. The crystal is a triclinic box with a C2 symmetry. I have built the unit cell, which has 4 copies of the protein, and add some water on top of the ones in the pdb. Then minimized and run positional restrained MD followed by a non restrained MD. The system crashed after ~600ps reporting of LINCS errors. > > Now I have minimized it before running; I have checked the > topology and could not find any error; I have also tried to run > it in shake and the system crashed as well; I also run the system > in NVT without any success. I guess this is a symptom to something like pressure problems, PBC issues or bad topology, but I could not find it. I also looked for an isolated water molecule which might have caused it, without any success. So I hope someone else can come with the bright idea I don’t have. The rate of water and protein is ~1 protein to 300 water molecules, In addition I add NaCl to neutralise the system and bring it to 0.1M concentration. Also here is my mdp file: integrator = md dt = 0.002 ; ps ! nsteps = 2500000 ; OPTIONS FOR BONDS ; Constrain control constraints = all-bonds ; Do not constrain the start configuration continuation = yes ; Type of constraint algorithm constraint-algorithm = lincs ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 100000 nstvout = 100000 nstfout = 100000 ; Output frequency and precision for xtc file nstxtcout = 2500 xtc-precision = 1000 ; Energy monitoring energygrps = Protein nstenergy = 1000 ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 5 ; ns algorithm (simple or grid) ns-type = Grid ; nblist cut-off rlist = 0.8 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = Reaction-Field rcoulomb = 1.4 epsilon_rf = 62 vdw-type = Cut-off ; cut-off lengths rvdw-switch = 0 rvdw = 1.4 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = no ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling tcoupl = berendsen ; Groups to couple separately, time constant (ps) and reference temperature (K) tc-grps = Protein solvent tau-t = 0.1 0.1 ref-t = 300 300 ; Pressure coupling Pcoupl = no Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; Do not generate velocities gen_vel = no ; Center of mass control nstcomm = 10000 ; Periodic boundary conditions pbc = xyz ; Mode for center of mass motion removal comm-mode = Linear ; Groups for center of mass motion removal comm-grps = system > Thanks in advance, > Itamar. > -- > > > "In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut > > =========================================== > | Itamar Kass, Ph.D. > | Postdoctoral Research Fellow > | > | Department of Biochemistry and Molecular Biology > | Building 77 Clayton Campus > | Wellington Road > | Monash University, > | Victoria 3800 > | Australia > | > | Tel: +61 3 9902 9376 > | Fax: +61 3 9902 9500 > | E-mail: [email protected] > ============================================ | ----------------------------------------------------------- > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
