Hi ALL,<br><br>Thanks Justin for your reply.<br>Now after solvating my CG system of protein in lipid bilayer, I did EM and the final energy values were reasonable. But while running MD I am getting the following error:<br>
<br>-----------------------------------------------------------------------------------<br>Fatal error:<br>Number of grid cells is zero. Probably the system and box collapsed<br>-----------------------------------------------------------------------------------<br>
<br>In the archives I found this error and possible solution "to check the structure". But that is for all-atom system and according to me my CG system is OK. But I am not sure about the mdp parameters that I got from a example script from MARTINI site for running lipid MD. So can you please check the mdp file and suggest a solution for this problem.<br>
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------<br>; STANDARD MD INPUT OPTIONS FOR MARTINI 2.0<br>
;<br>; for use with GROMACS 3.3<br>;<br><br>; VARIOUS PREPROCESSING OPTIONS = <br>title = Martini<br>cpp = /usr/bin/cpp<br><br>; RUN CONTROL PARAMETERS = <br>; MARTINI - Most simulations are stable with dt=40 fs,<br>
; some (especially rings) require 20-30 fs.<br>; The range of time steps used for parametrization <br>; is 20-40 fs, using smaller time steps is therefore not recommended.<br><br>integrator = md<br>; start time and timestep in ps<br>
tinit = 0.0<br>dt = 0.030<br>nsteps = 900000<br>; number of steps for center of mass motion removal = <br>nstcomm = 1<br>comm-grps = <br>
<br>; OUTPUT CONTROL OPTIONS = <br>; Output frequency for coords (x), velocities (v) and forces (f) = <br>nstxout = 5000<br>nstvout = 5000<br>nstfout = 0<br>; Output frequency for energies to log file and energy file = <br>
nstlog = 1000<br>nstenergy = 1000<br>; Output frequency and precision for xtc file = <br>nstxtcout = 1000<br>xtc_precision = 100<br>; This selects the subset of atoms for the xtc file. You can = <br>
; select multiple groups. By default all atoms will be written. = <br>xtc-grps = <br>; Selection of energy groups = <br>energygrps = <br><br>; NEIGHBORSEARCHING PARAMETERS = <br>; MARTINI - no need for more frequent updates <br>
; or larger neighborlist cut-off due<br>; to the use of shifted potential energy functions.<br><br>; nblist update frequency = <br>nstlist = 10<br>; ns algorithm (simple or grid) = <br>ns_type = grid<br>
; Periodic boundary conditions: xyz or none = <br>pbc = xyz<br>; nblist cut-off = <br>rlist = 1.2<br><br>; OPTIONS FOR ELECTROSTATICS AND VDW = <br>; MARTINI - vdw and electrostatic interactions are used<br>
; in their shifted forms. Changing to other types of<br>; electrostatics will affect the general performance of<br>; the model.<br><br>; Method for doing electrostatics = <br>coulombtype = Shift <br>rcoulomb_switch = 0.0<br>
rcoulomb = 1.2<br>; Dielectric constant (DC) for cut-off or DC of reaction field = <br>epsilon_r = 15<br>; Method for doing Van der Waals = <br>vdw_type = Shift <br>; cut-off lengths = <br>
rvdw_switch = 0.9<br>rvdw = 1.2<br>; Apply long range dispersion corrections for Energy and Pressure = <br>DispCorr = No<br><br>; OPTIONS FOR WEAK COUPLING ALGORITHMS = <br>
; MARTINI - normal temperature and pressure coupling schemes <br>; can be used. It is recommended to couple individual groups<br>; in your system seperately.<br><br>; Temperature coupling = <br>tcoupl = Berendsen<br>
; Groups to couple separately = <br>tc-grps = Protein DSPC W<br>; Time constant (ps) and reference temperature (K) = <br>tau_t = 0.3 0.3 0.3<br>ref_t = 315 315 315<br>
; Pressure coupling = <br>Pcoupl = berendsen <br>Pcoupltype = isotropic<br>; Time constant (ps), compressibility (1/bar) and reference P (bar) = <br>tau_p = 3.0 <br>
compressibility = 3e-5<br>ref_p = 1.0<br><br>; GENERATE VELOCITIES FOR STARTUP RUN = <br>gen_vel = no<br>gen_temp = 315<br>gen_seed = 666<br><br>
; OPTIONS FOR BONDS = <br>; MARTINI - for ring systems constraints are defined<br>; which are best handled using Lincs. <br><br>constraints = none <br>; Type of constraint algorithm = <br>constraint_algorithm = Lincs<br>
; Do not constrain the start configuration = <br>unconstrained_start = no<br>; Highest order in the expansion of the constraint coupling matrix = <br>lincs_order = 4<br>; Lincs will write a warning to the stderr if in one step a bond = <br>
; rotates over more degrees than = <br>lincs_warnangle = 30<br>--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------<br>
<br>Any suggestion is welcome.<br><br>Regards,<br><br>Anirban<br>