Hi Justin, Thanks for the reply. I am doing the energy minimization of Na K pump with PDB ID 3B8E using MARTINI forcefield. Here is my em.mdp file for the same. First I get the .gro file from my cleaned PDB file and then try to minimize the system using grompp and then when I do mdrun it gives me lincs warning and gives me segmentation fault.
; ; STANDARD MD INPUT OPTIONS FOR MARTINI 2.0 ; ; for use with GROMACS 3.3 ; ; VARIOUS PREPROCESSING OPTIONS = title = Martini cpp = /usr/bin/cpp ; RUN CONTROL PARAMETERS = ; MARTINI - Most simulations are stable with dt=40 fs, ; some (especially rings) require 20-30 fs. ; The range of time steps used for parametrization ; is 20-40 fs, using smaller time steps is therefore not recommended. integrator = steep ; start time and timestep in ps tinit = 0.0 dt = 0.030 nsteps = 1000 ; number of steps for center of mass motion removal = nstcomm = 1 comm-grps = ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 5000 nstvout = 5000 nstfout = 0 ; Output frequency for energies to log file and energy file = nstlog = 1000 nstenergy = 1000 ; Output frequency and precision for xtc file = nstxtcout = 1000 xtc_precision = 100 ; This selects the subset of atoms for the xtc file. You can = ; select multiple groups. By default all atoms will be written. = xtc-grps = ; Selection of energy groups = energygrps = ; NEIGHBORSEARCHING PARAMETERS = ; MARTINI - no need for more frequent updates ; or larger neighborlist cut-off due ; to the use of shifted potential energy functions. ; nblist update frequency = nstlist = 10 ; ns algorithm (simple or grid) = ns_type = grid ; Periodic boundary conditions: xyz or none = pbc = xyz ; nblist cut-off = rlist = 1.2 ; OPTIONS FOR ELECTROSTATICS AND VDW = ; MARTINI - vdw and electrostatic interactions are used ; in their shifted forms. Changing to other types of ; electrostatics will affect the general performance of ; the model. ; Method for doing electrostatics = coulombtype = Shift rcoulomb_switch = 0.0 rcoulomb = 1.2 ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon_r = 15 ; Method for doing Van der Waals = vdw_type = Shift ; cut-off lengths = rvdw_switch = 0.9 rvdw = 1.2 ; Apply long range dispersion corrections for Energy and Pressure = DispCorr = No ; OPTIONS FOR WEAK COUPLING ALGORITHMS = ; MARTINI - normal temperature and pressure coupling schemes ; can be used. It is recommended to couple individual groups ; in your system seperately. ; Temperature coupling = tcoupl = no Pcoupl = no ; GENERATE VELOCITIES FOR STARTUP RUN = gen_vel = no gen_temp = 320 gen_seed = 473529 ; OPTIONS FOR BONDS = ; MARTINI - for ring systems constraints are defined ; which are best handled using Lincs. constraints = none ; Type of constraint algorithm = constraint_algorithm = Lincs ; Do not constrain the start configuration = unconstrained_start = no ; Highest order in the expansion of the constraint coupling matrix = lincs_order = 4 ; Lincs will write a warning to the stderr if in one step a bond = ; rotates over more degrees than = lincs_warnangle = 30 On Tue, Sep 29, 2009 at 4:17 PM, Justin A. Lemkul <[email protected]> wrote: > > > sunny mishra wrote: > >> Hi, >> >> I have a quick question. My system exploded when I tried to run the >> simulation and it gives me the LINCS warning. I am using MARTINI forcefield >> and finally I get segmentation fault. I don't know that what are the factors >> do i need to change to get rid of the LINCS warning. Please let me know. I >> also tried changing the large Van Der Waal distance but it doesn't work >> either. Do you have any idea? >> >> > General answer: your system is unstable. Changing cutoffs haphazardly is a > recipe for failure; these values are often intimately linked to the validity > of the force field. You will probably have to provide more information on > what you are doing (system description, as well as your .mdp file). Now > that the mailing list search is functioning again (officially), you should > be able to search the list archive. LINCS errors are posted weekly, if not > daily sometimes! > > -Justin > > Sunny >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list [email protected] >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > _______________________________________________ > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php >
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